Soil microbes are critical for maintaining ecosystem function and terrestrial carbon, nitrogen, phosphorus and sulfur cycles. In order to elucidate the mechanism of bacterial community response to long-term fertilization, a long-term field experiment was conducted in fluvo-aquic soil in the North China Plain, in which four treatments were set up: no fertilization (CK), chemical fertilization (NPK), organic fertilization (OM) and their combination (NPKM). The composition and ecological function of soil bacterial community and their relationships with soil nutrients were determined and compared by using metagenome sequencing. The results indicated that OM and NPKM significantly increased the contents of soil total carbon, total nitrogen, organic carbon, and available phosphorus compared to CK and NPK (P&llt;0.05). The highest community diversity and richness indices were found in NPK. Also, different fertilization treatments significantly altered bacterial community structure. Further LEfSe analysis showed that Acidobacteria and Proteobacteria were enriched in OM and NPKM, respectively, and that both were key bacterial taxa involved in nutrient cycling. Long-term fertilization significantly increased the diversity of functional bacterial genes (P<0.05). Moreover, OM and NPKM reduced gene abundance related to carbon cycle, while affecting bacterial involvement in key processes of nitrogen, phosphorus and sulfur cycles. Mantel test showed that factors such as soil organic carbon, total nitrogen, total carbon, and available phosphorus were important for the structure and function of bacterial communities (P=0.001). The result provides a basis for rational fertilization application to regulate microorganisms to drive nutrient cycling in agricultural soils.