The change of hydrological rhythm will affect the stability and security of wetland ecosystems. In order to explore the influence of annually hydrology variation on the soil microbial functional traits, we selected the surface soils (0-20 cm) under three different vegetation types-Cynodon dactylon, Triarrhena lutarioriparia and Carex cinerascens as study objects from the Lake Poyang wetlands. The soil activity characteristics of microbial respiration, microbial biomass and soil enzymes in wetland soils were tested in three consecutive years. The effects of annually water level changes on soil microbial activities in different vegetation wetlands were analyzed. The results showed that:The contents of soil available nutrient sources (including organic matter, total phosphorus, and available phosphorus) was enhanced in high flow years, as well as soil microbial biomass, microbial entropy and hydrolase activities, which were beneficial to material circulation and transformation of the wetland ecosystem. Hydrological conditions affected the state of soil nutrients by affecting the growth of wetland vegetation, and further affected the soil microbial functional traits. Among various soil physicochemical factors, dissolved organic carbon was the most critical factor driving the change of microbial functional traits. Further analysis showed that the long-term historical hydrological cumulative effects represented by different vegetations had greater impact on the soil physicochemical properties and microbial functional traits than the pure hydrological changes annually.