Excessively using fertilizers poses serious problems such as environmental pollution, soil degeneration, and quality and yield reduction of vegetables. This study aimed to illustrate the effect of different organic manure and inorganic fertilizers on the characteristics of soil, and the growth, yield, and quality of non-heading Chinese cabbage. There were 28 treatments in the first experiment: no fertilization (CK), conventional fertilization (100% nitrogen T1), 20% reduction of total nitrogen (T2), 30% reduction of total nitrogen (T3), and 20% or 30% reduction of total nitrogen with four kinds of fertilizers and three kinds of dosages (24 treatments). Six treatments, being selected from the first experiment based on growth of plants, were further applied to the second experiment. The results of the second experiment showed that the pH, nitrate nitrogen, and organic matter content of soil treated by N2 (20% reduction of total nitrogen with 1500 kg·ha−1 No.1: Bacillus-enriched bio-organic fertilizer) were significantly enhanced compared with T1 (100% nitrogen). The N2-treated plants showed an 11.66% increase in root activity, 9.24% enhancement in yield, 5.79% increase in vitamin C (VC), and 47.87% decrease in nitrate content compared with T1. Nitrogen reduction with bio-organic fertilizer significantly increased the dominant phyla of Gemmatimonadetes and Chytridiomycota and significantly decreased Ascomycota, and increased the dominant genera of Gemmatimonas and Bacillus and decreased Fusarium, indicating that this treatment altered the microbial community composition of soil. Redundancy analysis (RDA) showed that AP (available phosphorus), OM (organic matter), and UREA (urease activity) of the soil were significantly correlated with microbial community structure. Yield was significantly, positively correlated with Rhodanobacter and Olpidium. In conclusion, nitrogen reduction with bio-organic fertilizer benefited growth, yield, and quality of non-heading Chinese cabbage by improving the soil quality.