Soil microorganisms are pivotal in global biogeochemical cycles, significantly influencing energy flow and climate regulation. The Deyeuxia angustifolia wetland in the Sanjiang Plain, northeastern China, represents a key ecological area, yet the impact of organic nitrogen (Urea) addition on its soil microbial community remains largely unexplored. This study delves into the assembly patterns and processes of soil microbial communities following seven years of urea addition in this wetland, utilizing high-throughput sequencing technology. Our findings reveal that urea addition leads to a decrease in soil pH and an increase in various soil nutrients, including dissolved organic carbon, total nitrogen, organic carbon, dissolved organic nitrogen, nitrate, and ammonia nitrogen. While urea addition significantly alters soil bacterial and fungal β-diversity, it does not affect their α-diversities. Comparative analysis across nitrogen treatments shows significant shifts in 24 bacterial and 21 fungal taxa. The abundance of a few bacterial genera (Bradyrhizobium and Haliangium) decreases with increasing N addition; while the abundance of a few fungal genera (Penicillium and Coniochaeta) increases with the increasing N addition. Random forest models revealed that rare genera (e.g., Syntrophorhabdus, Terrimonas, Galerina, and Mariannaea) also play an important role during organic nitrogen addition. Co-occurrence network analysis indicates a weakening interaction between bacteria and fungi with increased urea addition, accompanied by shifts in dominant bacterial and fungal phyla. Mantel test revealed a correlation between bacterial community diversity, network topology properties and various soil physico-chemical properties, while only network topology properties were correlated with soil physicochemical properties in the fungal community. Structural equation modeling (SEM) suggested that organic nitrogen addition affect soil bacterial and fungal structure by influencing plant diversity, plant biomass, and environmental factors. Community assembly analysis reveals a stochastic dominance in bacterial communities and a deterministic dominance in fungal communities under urea addition. Overall, this study enhances our understanding of soil microbial community responses to organic nitrogen addition in wetland ecosystems, offering insights for their sustainable management.