Obvious changes of hydrologic regimes occurred in wetland around the world, and it also were expected to arise in the following 100 years. This study examined the response of soil microbial functional structure and metabolic potential to early dry season (EDS) of Dongting Lake wetland, China. We measured the soil properties, microbial functional structure of samples E40, E20 and E0 (dry season arrived early by 40, 20 and 0 days, respectively). The results showed that the EDS caused the changes of functional structure: the functional genes of E40 had significantly higher abundance and diversity than those of E0, but no significant difference was found between those of E20 and E0. Functional genes associated with matter cycling and organic contaminant degradation (OCD) also were changed. It could cause the increase of the degradation of pesticides related compound of E20 and matter cycling and OCD of E40 (except no change in the phosphorus oxidation and the degradation of polycyclic aromatics and terpenoid).