The deep migration of soil nitrogen (N) poses a significant risk of N leaching, contributing to non-point-source pollution. This study examines the influence of microbial networks on the deep migration of chemical fertilizer N under varying irrigation management and multiple N fertilizer sources. A soil column experiment with eight treatments was conducted, utilizing ¹⁵N isotope labeling and metagenomic sequencing technology. The findings revealed that reduced irrigation significantly curbs the deep migration of chemical fertilizer N, and straw returning also mitigates this migration under conventional irrigation. Microbial network complexity and stability were markedly higher under reduced irrigation compared to conventional practices. Notably, network node count, average degree, and modularity exhibited significant negative correlations with the deep migration of chemical fertilizer N. The network topology indices, including node count, average clustering coefficient, average degree, modularity, and edge count, were found to be relatively more important for the deep migration of chemical fertilizer N. In conclusion, microbial networks play an important role in reducing the deep migration of chemical fertilizer N.