To obtain high maize yield (Zea mays L.), nitrogen (N) fertilizer is widely used across the world and has greatly altered soil microbial communities and influenced soil health. Increasing plant density is an effective strategy for increasing maize yield, while variations in soil microbial communities in response to plant density under high N levels have not been well-studied. In Northeast China, maize was grown at low (LD, 67,500 plants ha−1) and high (HD, 90,000 plants ha−1) densities, combined with three N application rates of 0, 200, and 400 kg N ha−1yr−1(N0, N200 and N400). Based on a six-year field experiment, key soil microbial characteristics and physicochemical properties of top soils (0–20 cm), as well as yield and vegetative parameters were examined. Compared with that of LD, the maize grain yield of HD increased 10.8 % across N application rates from 2012 to 2017 (P < 0.05), while no significant differences between N200 and N400 were observed. HD significantly increased microbial biomass carbon (MBC), microbial biomass N (MBN), and bacterial and fungal diversity at N400 (P < 0.05). Dominant bacterial phyla across all samples were Proteobacteria, Acidobacteria, Actinobacteria and Thaumarchaeota, and fungal phyla were Ascomycota, Basidiomycota and Zygomycota. Species composition of HD shared more similarity between N200 and N400 than that of LD. HD significantly increased the abundance of Nitrososphaera and reduced the abundance of Pseudomonas and Sphingobium. From LD to HD, ammonia-oxidizing archaea (AOA) gene abundance increased while nirK gene abundance decreased at all N application rates, and ammonia oxidizing bacteria (AOB) and nirS gene abundances decreased at N0 and N400 but increased at N200 (P < 0.05). Shoot biomass and N uptake were positively correlated with MBC and MBN but negatively correlated with microbial community diversity. HD directly increased root biomass and N uptake, then reduced soil N contents (NH4+-N, NO3–-N, and TN) and thus positively regulated soil microbial communities. Relative differences of diversity indexes and functional gene abundances between N application rates of HD were significantly lower than those of LD. Overall, our findings indicate that higher plant density of maize could mitigate the adverse effects of N fertilizer overuse on soil microbial communities, thus reconciling maize productivity and black soil health in Northeast China.