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−2·a−1 (denoted as CK, C1, C2, and C3, respectively). The results showed that a high-level N (24 gN·m−2·a−1) 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 NH4+ 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 Azospirillum and Desulfovibrio, which were typical N-fixing microorganisms. Conversely, the long-term N input was found to significantly increase the abundance of Nitrosospira and Clostridium_sensu_stricto_1, 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.