The aim of this study was to explore the long-term effects of biochar on improving soil fertility in farmland in the northern Xinjiang irrigation area. A three-year field trial with three treatments: no biochar application (B0), low biochar application (10 thm-2, B1), and high biochar application (20 thm-2, B2), was conducted to systematically analyze the effects of biochar on soil aggregate carbon and nitrogen components, enzyme activities, and microbial community structure. The results showed that when the biochar application rate was 10 t·hm-2, it exhibited the optimal soil improvement effect. Specifically, the organic carbon content in aggregates larger than 2 mm and smaller than 0.25 mm demonstrated an upward trend with the application of biochar. Among them, in the aggregates larger than 2 mm, the organic carbon content in treatment B1 was significantly increased by 44.05% compared to treatment B0. In the aggregates smaller than 0.25 mm, the organic carbon content initially increased and then decreased with the application of biochar, reaching the maximum in B1. Also, the total nitrogen content in aggregates larger than 2 mm first increased and then decreased with the application of biochar, reaching the highest level in B1. Furthermore, the findings indicated that the application of biochar increased the microbial biomass carbon and nitrogen in aggregates larger than 2 mm and in the range of 2~0.25 mm, while reducing the microbial biomass nitrogen in aggregates smaller than 0.25 mm. Meanwhile, the urease activity in all three types of aggregates showed an upward trend with the application of biochar. Under the three aggregate conditions, compared to B0, B1 increased the activity of urease by 14.53%, 5.43%, and 1.08%, respectively. In addition, catalase activity was highest under the B1 condition, increasing by 10.64%, 21.43%, and 23.4% compared to B0, respectively. Although sucrase activity slightly decreased, it still remained at a relatively high level, ensuring the supply of carbon sources. The application of biochar significantly enhanced the α-diversity (Shannon and Chao1 indices) of the soil bacterial community. This promoting effect was strengthened as the aggregate particle size decreased. Moreover, under the application rate of 10 t·hm-2 (B1), the improvement effect was relatively balanced. In contrast, the impact of biochar on the α-diversity of fungi was relatively weak. The Shannon index only increased slightly, and the Chao1 index showed no significant change, indicating that the fungal community was less sensitive to the application of biochar compared to the bacterial community. Under the conditions of this study, applying 10 t·hm-2 of biochar (B1) can increase the content of carbon and nitrogen components in soil aggregates of wheat fields while enhancing the abundance of beneficial microbial communities.