[Objective] Studing the effects of long-term-fertilization in wheat-corn rotation field with Lou soil on water stable aggregates and soil nutrient distribution in different sizes of aggregates, to provide a scientific basis for the evaluation of long term-fertilization on its improvement effect.[Methods] The wheat-corn rotation field with long-term application of chemical fertilizer was selected as the study site. The composition of aggregates was analyzed using the wet sieve method. Contents of organic carbon and nutrients in different sizes of aggregates were measured.[Results] Long-term application of chemical fertilizers significantly affected soil water stable aggregate contents. Long-term fertilization reduced the contents of >2 mm soil water stable aggregates, but increased <1 mm soil water stable aggregate contents. To a certain extent, the amount of organic carbon in water stable aggregates increased, but the organic carbon contents of 0.25~0.5 mm and <0.25 mm soil water stable aggregates under high nitrogen and phosphorus treatments were significantly lower than that of the low nitrogen and phosphorus treatment. The changing tendencies of contents of total nitrogen in soil water stable aggregates were essentially in agreement with organic carbon in soil water stable aggregates under different fertilization treatments. Distribution of phosphorus in different size soil water stable aggregates was even in no fertilization treatment. The difference of phosphorus content in each size soil water stable aggregate was insignificant under low nitrogen and phosphorus treatment, while the trend in high nitrogen and phosphorus treatment was not obvious. The total potassium contents of >2 mm soil water stable aggregates decreased due to long-term application of chemical fertilizer, whereas total potassium contents of <2 mm soil water stable aggregates increased under long-term application of fertilizer.[Conclusion] Soil water stable aggregates influenced the quantity of soil organic carbon and nitrogen. The contents of soil water stable aggregates, soil organic carbon and nitrogen of soil water stable aggregates varied irregularly under long-term application of nitrogen and phosphorus fertilizers. In addition, conservation and supply capacity of phosphorus and potassium in soil were affected by long-term application of nitrogen and phosphorus fertilizers. Therefore, reasonable use of chemical fertilizers and management were needed to improve the soil structure, maintain soil fertility and promote the sustainability of farmland productivity.