Ecological compensation is an effective means to solve the conflict of interests among trans-boundary river basin countries. How to determine the ecological compensation standard is the core of ecological compensation. On the basis of the emergy synthesis method, we developed an emergy-water resources ecological footprint model for trans-boundary river basin countries. Based on the calculation of ecosystem service value and consumption ecological value of trans-boundary river basin countries, the ecological spillover value of each basin country is obtained. From the perspective of supply and consumption, the ecological compensation standard in basin countries is determined by judging the supply and consumption status of ecological services and combining with the willingness to pay for ecological compensation. Taking the Lancang–Mekong River Basin as an example, the results show that (1) the ecosystem service value of the Lancang–Mekong River Basin countries from high to low is Laos, Cambodia, Thailand, China, Vietnam, and Myanmar; (2) in terms of ecosystem service value consumption, the order from high to low is Thailand, Cambodia, Vietnam, China, Laos, and Myanmar; and (3) Thailand and Vietnam, located in the lower reaches of the basin, belong to the consumers of ecological services, and based on the actual willingness to pay, they need to pay $46.913 billion and $1.699 billion, respectively.

With the rapid development of social economy and global climate warming, scarce transboundary water resources, as one of the basic resources for socio-economic development, have increasingly become the focus of basin countries. To investigate the socio-economic impacts of different water diversion quantity from transboundary river basins, we used a system dynamics (SD) model to reflect interactions between population, water resources, and socio-economic development, and applied it to a case study in Xinjiang to simulate its change tendency from 2011 to 2030 from the temporal dimension. Then, four water diversion quantity of transboundary river basins and four alternative socio-economic development patterns were designed to comprehensively evaluate these impacts of water diversion quantity change on the socio-economy of the region along the river under different socio-economic development patterns. The results indicate that (1) there was a positive correlation between water diversion quantity and the economic output value of the region along transboundary river basins, and the marginal benefit of transboundary water resources would decrease gradually; (2) considering the difficulty of water diversion from transboundary river basins and the protection of downstream water use and ecological health of transboundary river basins, we believe that increasing the transboundary water resources by 20% was more conducive to the sustainable development of Xinjiang’s socio-economy; (3) through the comparison of dynamic evolutions of socio-economic development and water impacts under four socio-economic development patterns, it is best for Xinjiang to plan its future development in the coordinated development of economic-resource scenario. Following this scenario, not only would the total output value of the socio-economy be better than other scenarios, but this also helps to alleviate the contradiction between the water supply and demand, which expected there would be a water shortage of 1.04 billion m³ in 2029 under 20% increase in water diversion quantity. Therefore, appropriate water diversion quantity, reasonable adjustment of industrial production growth rate, reduction of water consumption quotas of different industries and domestic water quota, and improvement of collection and treatment rate for sewage should be given priority in water resources management decision-making in Xinjiang or other arid regions along transboundary river basins.

The issue of trans-boundary water conflict has become an important factor affecting the relations between basin countries. The key to solve the current conflict problem is to realize the fair and reasonable allocation of trans-boundary water resources. Based on the satisfaction perspective, we developed an asymmetric Nash negotiation model to obtain an optimal and feasible allocation scheme for the trans-boundary water resources. Firstly, based on the two international water laws, we analyzed the influencing factors including water demand differences, resource endowment differences, and water efficiency differences, and by combing with the flexible weight constraint, we built the fair and reasonable allocation pattern for trans-boundary water resources. Secondly, under the constraint of the allocation pattern, we determined the ideal negotiation scheme of each basin country by considering their selection preference. Thirdly, we built a satisfaction degree function and established an asymmetric Nash negotiation model. This is used to build a fair negotiation mechanism among basin countries, and the allocation scheme after negotiation is regarded as the optimal allocation scheme. Lastly, we took the Lancang–Mekong river basin as an example. For this example, the results indicate the following: (1) after considering multiple factors comprehensively, China and Thailand obtained a higher proportion of trans-boundary water resource quota under different preference scenarios, while Myanmar obtained a lower proportion of trans-boundary water resource quota; (2) taking each basin country as the negotiation agent, the optimal allocation scheme with the introduction of fair negotiation mechanism has a higher degree of satisfaction, with an average of over 87.19%, which is more stable and easy to be accepted by all basin countries; (3) from the perspective of the change rate and the average satisfaction of the basin countries, the optimal allocation scheme under the resource endowment preference scenario obtained the highest satisfaction among basin countries. This study aims to improve the practicability and acceptability of trans-boundary water resources allocation, thus providing technical support for reducing trans-boundary water resources conflicts.