Biochar incorporation is a widespread approach for soil improvement and soil carbon sequestration. However, there have only been a few studies on the effects of large-scale biochar incorporation on the estuarine wetland soil. To assess the different rates and incorporation times of biochar effects on the soil carbon cycle, the effects and mechanisms of biochar actions on soil respiration and plant growth were clarified via an outdoor control experiment that analyzed the soil microbial activity and community structure of estuarine wetland soil. The results unconventionally showed that a higher rate (238.82 g·kg−1) of biochar incorporation achieved stimulated soil respiration compared to lower incorporation rates (9.14 g·kg−1, 23.89 g·kg−1, 47.79 g·kg−1 and 143.36 g·kg−1) and was 38.9%, −21.8%, and 6.23% higher than the soil respiration of the control on three incorporation months. The soil microbial biomass (45.54% in the higher rate of biochar incorporation soil than the control) and the activities of β-glucosidase enzymes (25.4% higher in the higher rate of biochar incorporation soil than the control) explained these differences in soil respiration. This phenomenon was confirmed to be a result of provoking the bacteria of a heterotroph or from a lower humification ability, which enhanced organic carbon degradation in a large amount of biochar incorporation soil. In conclusion, even large-scale biochar incorporation may introduce more stable carbon to the soil, and the carbon sink of estuarine wetland soil may weaken due to the greater carbon output generated in its specific soil microbial species.