Water rights trading is an important way to solve the problem of water shortage by market mechanism. The allocation of water rights among ecological water, energy water, and grain planting water are the basis of the regional water rights trade. In this paper, the concept of coordinated development of water–ecology–energy–food is proposed. We build a water rights allocation model with fairness, efficiency, and coordinated development as the goal, to achieve water security for various industries. Taking Yinchuan city as an example, the results showed that compared with the current water rights the water rights of life increased by 1.07%, the water rights of ecology increased by 1.85%, the water rights of energy industry decreased by 1.09%, the water rights of food planting decreased by 3.27%, the water rights of other agriculture increased by 0.83%, and the water rights of the general industry increased by 0.65%. After the allocation of water rights, the cooperativity of water–ecology–energy–food increased by 7.56%, and the total value of water resources in various industries increased by 2.31 × 10⁸ CNY. A new water rights allocation model is developed in this paper, which can provide a reference for the allocation of water rights among regional industries.