In order to investigate the impact of microorganism in constructed wetland on purification efficiencies for slightly polluted river water in Three Gorges Reservoir Region, four horizontal subsurface flow wetlands planted with Arundo domax, Acorus calamus, Ipomoea aquatica and without plants (blank) were built in situ next to the Lushan River. The distribution of microbial basic flora and function flora in the wetlands were monitored, purification efficiencies of the constructed wetland systems were studied, and the correlation between microorganism and removal rates of pollutants were analyzed. The results showed that the experimental wetlands were adaptive to variation of inflow quality and quantity, and the removal efficiency of pollutants could be improved by planting hydrophytes. Microbial population in the planted wetlands was more than that in the blank wetland. There was positive correlation between microorganism quantity and temperature in all four wetlands, and quantity of ammonifying bacteria, nitrifying bacteria and denitrifying bacteria decreased significantly with the decline of temperature. There was conspicuous positive correlation between fungus population and removal of ammonia in summer, as well as bacteria population and removal of CODMn. It is similar positive correlation between denitrifying bacteria population and removal of total nitrogen in winter.