Plant aboveground biomass, total organic carbon( TOC), microbial biomass carbon( MBC), basal respiration( BR), microbial quotient (Cmic/Corg) and metabolic quotient (qCO2) in 0-15 cm and 15-50 cm marsh soil of Calamagrostis angustifolia under different water levels were investigated with controlled experiment. The result showed that water level exerted significant effect on plant biomass, which was the highest under 10 cm waterlogged level and of higher productivity under 0-20 cm waterlogged level. TOC, MBC, BR, Cmic/Corg and qCO2 differed significantly under different water levels. BR and TOC responded to different waterlogged levels in the same way. BR and TOC of 0-15 cm marsh soil were the highest under 0 cm waterlogged level, however, BR and TOC of 15-50 cm marsh soil decreased respectively with increasing water, which was corresponding with soil MBC and Cmic/Corg and qCO2 increased with increasing water. As a result, microbial community is altered and microbial activity is decreasing by increasing waterlogged level, and microbial activity is the lowest under 30 cm waterlogged level, which affects organic carbon accumulation and decomposition.