Plastic film mulching (PM) cultivation is an important measure to alleviate the seasonal shortage of water resources. Long‐term nitrogen (N) fertilization under PM cultivation may be more conducive to enhance the ecological relationship between microbial communities involved in nutrient cycling. In this study, the effects of long‐term application of chemical N fertilizer (common prilled urea [PU]) or no N fertilization on the microbial community composition under the traditional flooding (TF) cultivation and PM cultivation were comparatively analyzed. The results demonstrated that water regimes had significant effects on all soil properties except alkali‐hydrolyzable N. Compared with TF cultivation, PM cultivation increased pH and available phosphorus (AP) by 1.14 and 13.67%, respectively, and decreased organic matter and available potassium (AK) by 6.07 and 8.39%, respectively. Nitrogen fertilization levels had significant effects on soil AP and AK, with increases of 1.39 and 1.82 mg kg−1 in PU treatment compared with CK, respectively. Neither water regime nor N fertilization level had a significant influence on soil microbial richness (Chao index) and diversity (Shannon index). However, water regimes played critical roles in driving microbial community changes. Network analysis showed that the microbial community had nonrandom co‐occurrence pattern. Myrmecridium, Defluviicoccus, Emericellopsis, Pseudarthrobacter, and Syntrophorhabdus were the keystone taxa. A higher relative abundance of Defluviicoccus, Emericellopsis, and Syntrophorhabdus was observed in the CKPM treatment, and a higher relative abundance of Myrmecridium and Pseudarthrobacter was observed in the PUPM treatment. Therefore, PM cultivation is an effective measure to improve potential beneficial taxa of soil microbial communities.