Abstract: Microbial Nitrogen Use Efficiency (MNUE) reflects the proportion of absorbed nitrogen (N) allocated by microorganisms between growth metabolism and mineralization. As regulators of the conversion of soil organic N to inorganic N, MNUE governs the storage of absorbed N as organic matter within microbial biomass or its release into the soil as inorganic N. This process influences crop uptake and utilization of soil N. Nevertheless, in highly disturbed agricultural systems, the variability characteristics of MNUE and its underlying regulatory mechanisms remain inadequately understood, thereby limiting the scientific development of N management strategies for farmland soils. This review examines MNUE, focusing on the key factors and regulatory mechanisms governing it under different agricultural management practices. Overall, MNUE exhibits high variability within agricultural systems. This heterogeneity is primarily influenced by agricultural management practices (e.g., fertilization and tillage), soil physicochemical properties, microbial community structure, and environmental factors. The combined effects of these factors alter microbial N acquisition strategies by influencing soil pH, nutrient availability, microbial community composition, soil moisture content, oxygen levels, and temperature, ultimately leading to changes in MNUE. Currently, research predominantly focuses on controlled laboratory cultures or short-term field trials, lacking a systematic understanding of how different agricultural management practices affect MNUE across watershed and temporal scales. Future efforts should strengthen long-term observations across diverse soil types and climatic conditions. Integrating techniques such as metagenomics and metabolomics will elucidate the intrinsic linkages between key functional microorganisms, their N allocation strategies, and MNUE, thereby revealing the spatiotemporal heterogeneity of soil microbial N utilisation in agricultural fields.