Soil aggregates are the material basis of soil structure and important carriers of nutrients. Long-term application of organic and inorganic fertilizers can affect the composition of soil aggregates to varying degrees, which in turn affects the distribution and storage of soil nutrients. We report the results of a 15-year long-term field-based test of aeolian sandy soil and used the wet sieve method to analyze the stability of water-stable aggregates, as well as the distribution characteristics of nutrients in different particle size aggregates. Our results show that long-term application of organic fertilizer (M3) and combined organic–inorganic treatments (NPK1-M1, NPK1-M2, and NPK1-M3) help to increase the amount of organic carbon, inorganic carbon, and cation exchange in the macro-aggregates, and the improvement rates are 92–103%, 8–28%, and 74–85%, respectively. The organic content of the fertilizers also promotes the formation of macro-aggregates, and the stability of aggregates increase from 0.24 to 0.45. In contrast, the application of inorganic fertilizers (NPK1, NPK2, and NPK3) has no marked effect on the formation and stability of macro-aggregates; the application of inorganic fertilizers can merely maintain the organic carbon content of the soil. Correlation analysis shows that the application of organic fertilizers and chemical (inorganic) fertilizers containing phosphorus and potassium can markedly increase the content and reserves of available phosphorus and potassium across all aggregate sizes, and there is a significant positive correlation between these parameters and the amount of applied fertilizer (p < 0.05). Aggregates of various sizes in aeolian sandy soils in arid areas have the potential for greater nutrient storage. Therefore, organic fertilizers can be used in the agricultural production process to improve soil structure and fertility.

The desert oasis is one of the major grain production areas in arid land, and many intensive farming practices have been adopted to improve the land utilization in the agriculture system. However, there remains little consensus on how to improve such farming practices for increasing both productivity and environment benefits in this system. A 4-year experiment was conducted in a typical desert oasis farmland to determine the effects of the farming practices on crop yield, soil carbon (C) and nitrogen (N) accumulation, and carbon footprint (CF). The farming practices included two tillage patterns: conventional (CT) and reduced tillage (RT), two cropping patterns: continuous (Con) and rotation cropping (Rot), and two mulching pattern: film (F) and straw mulching (S) with eight combined treatments. The RT did not significant decrease crop yield but increase soil C and N accumulation rate by 59% and 130%, and thus decrease CF for crop production compared with the CT. S can also improve soil C and N accumulation, and cause low CF for crop production, but leading to 14–41% decrease in maize yield compared with F. Rot result in a 14% increase on maize yield also has extra benefit to decrease CF for crop production, but no significant effect on soil C and N accumulation compared with Con. Our study adds a reasonable perspective on how to improve the conventional farming systems in desert oasis, the information about RT, straw mulching, and maize–soybean rotation have positive effect on improving soil quality and decreasing CF for crop production in this desert soil area is critical to develop the sustainable agriculture system in this desert oasis farmland, which both maintaining crop productivity and minimizing negative environmental impacts.