Carbon gas flux is important for studies on carbon dynamics in mangroves, but the controlling factors have not always been sufficiently understood. In this study, it is suggested that sediment carbon dioxide (CO2) fluxes in a natural mangrove in Southern China are controlled by tidal positions, seasons, species, the densities of crab burrows and pneumatophores, light conditions and sediment temperature. All these factors account for 51.47% variation in CO2 flux from the sediment–air interface. CO2 flux generally decreased along the tidal position from landward to seaward, and was higher in the dry season than in the wet season. CO2 flux was highest in Avicennia marina (grey mangrove) in comparison with Aegiceras corniculatum (river mangrove) and Kandelia obovata. Pneumatophores and crab burrows promoted sediment CO2 flux in the mangrove at a rate of 18.29 and 15.52 mmol m−2 d−1. Dark flux was higher than light flux. Sediment temperature has a negative influence on CO2 flux. Pneumatophores explain the most variation (13.9%) in CO2 flux among the above factors. Our study suggests that the photosynthesis activity of microphytobenthos is an important factor driving the change of CO2 emissions in this natural mangrove. This is of great significance for the study and for the full exploitation of the carbon sink potential of mangroves.