This study was performed to provide a comprehensive assessment of the pollution of soil heavy metal(loid)s (HMs) and the relationships between HMs (including As, Cd, Cr, Cu, Ni, Se, Pb, Hg, and Mn) and soil microorganisms in the different utilized types of wetland soils (agricultural soils (AS), natural wetland soils (NWS), and restored wetland soils (RWS)). Our results indicated that As and Cd in the studied region accumulated to different degrees in AS, NWS, and RWS. The microbial community compositions and heatmaps showed that the compositions of bacterial, fungal, and archaeal communities had differences in various degrees. A comprehensive assessment was performed including the geoaccumulation index (Igeo), the pollution load index (PLI), and the potential ecological risk index (ERI) to evaluate the pollution of HMs. Based on the results, Cd and As were identified as the major pollutants that contributed to the potential ecological risk in AS, NWS, and RWS. The co-occurrence network analysis indicated that the bacterial genera Bryobacter and Acidothermus, the fungal genera Fusarium and Anguillospor, and the archaeal unclassified genus Nitrososphaeraceae were the key taxa in the microbial networks. Based on the interactive forward selection method in redundancy analysis (RDA), it could be concluded that microbial community compositions were mainly controlled by As.