Soil microbes are critical for maintaining ecosystem function and terrestrial carbon, nitrogen, phosphorus and sulfur cycles. This study was conducted to elucidate the mechanism of bacterial community response to bacterial community to long-term fertilization. To this end, the composition and ecological function of soil bacterial communities was analyzed, and their relationships with soil nutrients were investigated in long-term chemical fertilization (NPK), organic fertilization (OM) and chemical fertilization in combination with organic fertilization (NPKM). This investigation was performed using metagenome sequencing in a fluvo-aquic soil experiment with long-term fertilization treatments in the North China Plain. The results indicated that long-term organic fertilization significantly increased soil TC, TN, SOC, AP compared to the no fertilization and chemical fertilization treatment (P<0.05). The highest community diversity and richness indices were found in the chemical fertilization treatment. Also, different fertilization treatments significantly altered bacterial community structure. Further LEfSe analysis showed that Acidobacteria and Proteobacteria were enriched in the NPKM and OM treatments, 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, long-term organic fertilization 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 SOC, TN, TC and AP were important for the structure and function of bacterial communities (P=0.001). The result provided a basis for rational fertilization application to regulate microorganisms to drive nutrient cycling in agricultural soils.