In order to solve the problem of the decline of farmland soil fertility in the irrigation area of northern Xinjiang and the serious impact of agricultural sustainability, the impact of different biochar application rates on the soil fertility of farmland in the irrigation area of northern Xinjiang was studied. In this study, we focused on the effects of biochar application on the carbon and nitrogen composition and microbial community composition of soil aggregates after three years of application, aiming to clarify the continuous effect of biochar application in farmland in northern Xinjiang to improve soil structure and soil fertility. The changes of organic carbon, total nitrogen, microbial biomass carbon, microbial biomass nitrogen, soil enzyme activities (catalase, urease, sucrase) and microbial diversity of soil aggregates under different treatments were compared and analyzed without biochar (B0), biochar dosage of 10 t.hm-2 (B1) and biochar dosage of 20 t.hm-2 (B2). The results showed that the soil improvement effect of biochar was the best when the application rate was 10 t.hm-2. Specifically, the organic carbon content in the aggregates > 2 mm and 0.25-2 mm aggregates showed an upward trend with the application of biochar. B2 increased by 67.22% and 23.82% compared with B0, respectively, < organic carbon of 0.25 mm aggregate increased first and then decreased with the application of biochar, reaching the highest in B1, and B1 increased by 6.32% compared with B0 treatment, and the total nitrogen of 0.25 mm and < 0.25 mm aggregate reached the highest in B2 with the upward trend of biochar>< 0.25 mm aggregate microbial biomass nitrogen. At the same time, the urease activities of the three agglomerates reached the highest under the B2 biochar dosage, which increased by 16.01%, 28.26% and 11.5%, respectively, compared with B0. Catalase reached the highest level under B1 conditions, which were 10.64%, 21.43% and 23.4% higher than those of B0, respectively. Sucrase showed a downward trend with biochar application, and the B2 treatment of the three aggregates decreased by 8.36%, 8.53% and 23.53%, respectively, compared with the B0 treatment. Biochar application could increase the α diversity of soil bacteria and increase the relative abundance of microphyta wart, but there was no significant difference in microbial composition in different aggregates under the same biochar application conditions. The soil bacterial network was positively correlated under different biochar application rates, and Actinomycetes played a major role in all particle size aggregates, and biochar application could improve the network complexity of microorganisms in soil aggregates > 2 mm and 0.25-2 mm particle sizes. Under the conditions of this study, the application of 10 t.hm-2 biochar (B1) for three years could effectively increase the content of carbon and nitrogen components in wheat soil aggregates and microbial diversity, effectively improve soil structure, and provide data support and theoretical basis for further exploring the application of biochar in farmland in northern Xinjiang irrigation area to improve soil fertility and promote carbon sequestration and emission reduction.