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Slow- and controlled-release (SCR) nitrogen (N) fertilizers improve crop production and N utilization efficiency. However, responses of biological soil characteristics to the long-term application of N fertilizer have received little attention. In this work, a five-year field experiment was performed to assess the influence of different N fertilizer treatments (no N fertilizer application [CK] and applications of polymer-sulfur coated urea [PSCU], conventional prilled urea [PU], and urea-formaldehyde [UF]) on soil microbial communities in yellow clayey paddy soils in southern China. The types of N fertilizers had a stronger impact on soil bacterial diversity and community structure than fungal diversity and community structure. The soil microbial communities of PU and UF treatments did not differ from those of CK regarding alpha diversity indices. However, the PSCU treatment significantly decreased the Shannon index by 2.16% for bacteria but had no significant effect on the Shannon index of fungi. This might be due to the application of PSCU significantly reducing the soil pH by 0.16 units compared to CK and leading to soil acidification. Co-occurrence network analysis determined the keystone species mainly belonging to Proteobacteria and Ascomycota. Notably, these keystone species played an important role in PSCU-treated soils. Soil Ca2+, Na+, and NH 4 + were the main determinants of microbial network stability. These results contribute to our understanding of how SCR-N fertilizers impact soil microorganisms. • The application of polymer-sulfur coated urea significantly reduced soil pH. • Nitrogen fertilizer types had more significant effects on soil bacterial diversity. • Nitrogen fertilizer types significantly affected soil bacterial community composition. • Soil nutrient availability played critical role in driving microbial community change. [ABSTRACT FROM AUTHOR]