Increased nitrogen (N) input from natural factors and human activities may negatively impact the health of marsh wetlands. However, the understanding of how exogenous N affects the ecosystem remains limited. We selected the soil bacterial community as the index of ecosystem health and performed a long-term N input experiment, including four N levels of 0, 6, 12, and 24 gN·m·a (denoted as CK, C1, C2, and C3, respectively). The results showed that a high-level N (24 gN·m·a) input could significantly reduce the Chao index and ACE index for the bacterial community and inhibit some dominant microorganisms. The RDA results indicated that TN and NH were the critical factors influencing the soil microbial community under the long-term N input. Moreover, the long-term N input was found to significantly reduce the abundance of and , which were typical N-fixing microorganisms. Conversely, the long-term N input was found to significantly increase the abundance of and , which were typical nitrifying and denitrifying microorganisms. Increased soil N content has been suggested to inhibit the N fixation function of the wetland and exert a positive effect on the processes of nitrification and denitrification in the wetland ecosystem. Our research can be used to improve strategies to protect wetland health.