Soil carbon storage plays a crucial role in mitigating the climate warming and is significantly impacted by the land use pattern. To better understand soil carbon stability and the underlying microbial mechanism, based on qPCR, ELISA, and fluorescence techniques, the effects of land use changes on soil microbial abundance, enzyme activity, and soil carbon storage were investigated in the complex ecosystems of cropland, forestland, and wetland along three typical river (Wolvlan river, Bielahong river, Wusuli river) basin in Sanjiang Plain, China. We hypothesised that croplands soil carbon storage is lower than forestlands and wetlands, which is regulated by soil water content, microbe and enzyme activity. Results showed that topsoil TC in wetlands (85.54 mg·g−1) was higher than those in croplands (33.46 mg·g−1) and forestlands (46.13 mg·g−1). Topsoil water content increased 73.90 % and 71.64 % in wetlands than in farmland and forestlands, respectively. Additionally, reclamation diminished topsoil carbon storage. In croplands, soil dissolved organic carbon, microbial biomass carbon, microbial biomass nitrogen, available nitrogen, bacterial abundance, and soil enzymes (i.e., RubisCO, β-glucosidase, cellobiohydrolase, 1,4-N-acetylglucosaminidase and acid phosphatase) activities were substantially lower than those in wetlands. Structural equation modeling showed that soil carbon storage was positively related to soil water content and RubisCO activity but negatively related to soil bacterial abundance. Soil water content had the largest standardised total positive effect coefficient and indirectly influenced soil carbon storage by affecting RubisCO activity. Soil depth had a greater effect on SMC, hydrolase and site had a greater effect on bacteria and fungi abundance. The results highlight that the alteration of carbon fixing enzyme activity by soil water content is a crucial mechanism for soil carbon sequestration in response to land-use change. Management strategies that conserve natural wetlands, increase soil water content and minimize land disturbance would be effective in maintaining soil carbon stocks.