The emerging environment-associated issues due to the overuse of inorganic fertilizers in agricultural production are of global concern despite the benefit of high yields. Eco-friendly organic materials with the capability to fertilize soil are encouraged to partially replace mineral fertilizer. The N cycle conducted by soil microorganisms is the most important biogeochemical process, dictating the N bioavailability in farmland ecosystems; however, little is known about how organic material amendment affects soil microbial N cycling under chemical fertilizer reduction. Hence, a fixed field trial with five fertilization practices was implemented to experimentally alter microorganisms essential for the soil N cycle, including conventional chemical fertilization (NPK), reduced chemical fertilization (NPKR), reduced chemical fertilization plus straw (NPKRS), reduced chemical fertilization plus organic fertilizer (NPKRO), and reduced chemical fertilization plus organic fertilizer and straw (NPKROS). The microbial N-cycling gene abundances and associated N-converting genetic potentials were evaluated using real-time quantitative PCR. In comparison to conventional chemical fertilization (NPK), organic addition significantly increased the amounts of heterotrophic microbes involved in organic N decomposition, N fixation, and N reduction; however, it reduced autotrophic microbes performing ammonia oxidization. Consequently, the overall proportion of heterotrophic microbes was remarkably enhanced, and the autotrophic proportion was correspondingly lowered. The fertilization practice shift significantly improved N fixation and gaseous N emission potentials, whereas it suppressed NO leaching potential. A significant discrepancy among five fertilization treatments was observed based on functional gene abundances (PERMANOVA, =0.002),as revealed by distance-based redundancy analysis (db-RDA), with NH as the dominant factor. Organic fertilizer addition was beneficial for heterotrophic N functional microorganisms, with simultaneous input of straw augmenting such an effect. Pearson's correlation analysis revealed that N storage and gaseous N emission potentials were both substantially negatively correlated with NH; NO leaching potential was notably negatively associated with SOC and TN but significantly related to NH. In conclusion, chemical fertilizer reduction combined with organic material amendments, a main fertilization recommendation, may enhance soil N storage, diminish N loss by leaching, and mitigate the environmental risk of NO emission. This deserves attention considering that healthy and sustainable agricultural soil environment can be cultivated from the view of microbial N-cycling.