The application of green manure (GM) and nitrogen (N) fertilizer strategies plays pivotal roles in regulating soil N pools within the winter wheat (Triticum aestivum L.) cropping system. However, the impacts and underlying mechanisms of these strategies on soil organic N (SON) fractions and microbial community composition in drylands, as well as the relationships between microorganisms and SON fractions, remain unclear. To address this, an 8-year field experiment was conducted to investigate the effects of three GM treatments [black bean (BB, Phaseolus vulgaris L.), rapeseed (RS, Brassica napus L.), and fallow (FW, control)] and three N fertilizer levels (N0, N120, and N240) on soil N pools, wheat yield, and microbial community composition on the Loess Plateau of China. Results indicated that both N fertilizer and GM treatments increased the contents of soil total N (TN), NO3- N, microbial biomass N (MBN), and total hydrolysable-N (AHN). Specifically, growing BB as a GM crop significantly enhanced the AHN content by 13.3 %, primarily through increases in amino acid-N (AAN), hydrolysable NH4+-N (AN), and amino sugar-N (ASN). Notably, N fertilization reduced soil microbial interactions and bacterial diversity. However, GM cultivation mitigated the adverse effects of N fertilization on soil microbial communities and facilitated the microbial transformation of excessive mineral N into MBN. Compared to FW-N240, the cultivation of BB as GM coupled with reduced N fertilization not only increased wheat yield but also reduced N2O emissions. However, cultivating RS reduced N2O emissions and sustained wheat yield at the high N level (N240). Overall, integrating leguminous GMs with moderate N application (N120) enhanced soil N availability by promoting microbial-mediated N cycling, providing a sustainable strategy to regulate the N recycling process to enhance wheat productivity and soil fertility in dryland agroecosystems.