Abstract: During the period from July 2014 to July 2015, we collected the surface sediment samples from the intertidal mudflat of the Fujian Zhangjiang Estuary Mangrove National Nature Reserve in the subtropical area. We are aiming to reveal the influence of environmental factors on the gross primary production of microphytobenthos, community respiration, and net community production, and its underlying mechanism. The results showed that the annually-average gross primary production of microphytobenthos was (2.4±0.8)mmol C/(m²·h), and the variability was positively correlated with temperature with character of higher value in summer but lower in winter. Temperature has been considered as the major environmental factor controlling the change of gross primary production in the study area. The community respiration rate in the sediment of mangrove forest tends to be high because of litterfall. Thus, the community generally shows higher frequency of negative net production in some months of autumn, winter and spring. Howere, the annually-average net community production was (0.5±1.8)mmol C/（m²·h）, indicating the balanced state of CO₂ budget. Our study shows that the pattern of CO₂ source and sink in the sediment of mangrove habitats is profoundly affected by the primary productivity of microphytobenthos, which has played important roles in the carbon cycling of mangrove ecosystem.