Purpose <p>The amendment of biochar has been proposed as a promising means to enhance soil fertility and crop productivity. However, the interactive impacts of biochar and nitrogen (N) fertilizer, especially controlled-release N fertilizer, on soil microbial community remains poorly understood.</p> Methods <p>Therefore, a 3-year field trial was conducted to systematically reveal the combined effects of biochar (0 and 3 t biochar C hm^− 2 season^− 1) and N fertilizer (urea and controlled-release urea, CRU) on soil bacterial community structure, co-occurrence network, and maize-wheat yields.</p> Results <p>Results showed that the co-application of biochar and N fertilizer, especially CRU, is more conducive to improving soil organic matter (SOM) and NO₃⁻-N content. The responses of soil bacteria composition, diversity, and co-occurrence network complexity to biochar are closely related to N fertilizer type. In particular, the combined application of biochar and CRU decreases soil bacterial diversity and reduces the co-occurrence network complexity while deepening the cooperation between soil microorganisms. Biochar and CRU fertilization increased the abundance of Bacteroidetes, Proteobacteria, and Nitrospirae but decreased the Actinobacteria, Chloroflexi, and Gemmatimonadetes abundance. Co-application of biochar and CRU resulted in the highest maize and wheat yields, which were 3.0–25.3% and 1.8–27.1%, respectively, higher than other fertilization treatments.</p> Conclusions <p>These findings indicate that the co-application of biochar and CRU holds strong potential for promoting wheat-maize productivity in the North China Plain.</p>