Microbial species have different niche breadth, leading to distinct habitat ranges. Specialists have narrow niche breadth and high habitat specificity in comparison with the generalists, which possess extensive habitat ranges. Since specialists have low probabilities to occur in various habitats at a specific spatio-temporal scale, communities with different ratios of specialists and generalists may exhibit different species co-occurrence patterns and functional characteristics. However, it is still not clear how the assemblages of specialists and generalists can affect microbial co-occurrence and functional potential at a large biogeographical scale. In this study, we explored the relationship between microbial habitat specificity and the co-occurrence patterns of prokaryotic communities in Chinese wetland soils and the contribution of functional profiles to this relationship. We first identified some specialists and generalists which hold significant roles in the co-occurrence network. Then, we found that communities with more specialists have more simple co-occurrence patterns (fewer linkages in network) than those with more generalists. Soil electrical conductivity was the most significant abiotic factor in structuring this relationship. The biological mechanisms that contribute to this relationship were closely associated with functional differences of taxa. With the increase of specialists in communities, aerobic ammonia oxidation and cellulolysis guilds decreased, and photoautotrophy and sulfate/sulfide respiration populations increased. Furthermore, the abundances of metabolic pathways altered along with the abiotic gradients (e.g., conductivity and pH), including carbohydrate degradation, fermentation, inorganic nutrient metabolism and stress resistance-related pathways. Especially, there were higher abundances of metabolism-related pathways in communities with more specialists compared to those with more generalists. Functional differences at traits, genes, and metabolic pathways reflected the characteristics of microbial co-occurrence patterns and biogeochemical cycles of habitats. In summary, microbial habitat-specificity can modulate the co-occurrence patterns of prokaryotic communities along the environmental gradients in wetland soils. Our findings provide a mechanistic understanding on how microbial niche breadth can affect microbial co-occurrence in wetland soils.