Overuse of chemical fertilizer (CF) causes damage to soil and the environment. To reveal the process of the response of crop rhizospheric and bulk soil fertility and the bacterial community to long-term CF conditions, CF application and nonfertilization (CK, control) treatments were used in a long-term (12-year) fertilization experiment. Long-term CF application significantly increased the soil organic matter, total nitrogen, and available phosphorus contents (p < 0.05), increased the available nitrogen (AN) and potassium (AK) contents to varying degrees, and decreased the soil pH in both rice rhizospheric soil and bulk soil. In addition, the bacterial Shannon and Ace indices in rice rhizospheric soil under the CF treatment were all higher than those under the control (CK) treatment, and the bulk soil bacteria showed the opposite trend. The LEfSe results showed that unidentified_Gammaproteobacteria and Geobacter (genera) were significantly enriched in the rhizospheric and bulk soil of rice under the CK treatment, respectively. Gemmatimonadetes (phylum) and Nitrospirae (phylum) + Thiobacillus (genus) were significantly enriched in the rice rhizospheric and bulk soil under the CF treatment. Only AK and AN had strong positive correlations with soil bacteria. Long-term CF application accelerated the migration of soil bacteria from the bulk soil to the rhizosphere, thus improving soil fertility and nutrient cycling.