Aquaculture, particularly shellfish ponds, has expanded dramatically and become a major cause of mangrove deforestation and “blue carbon” loss in China. We present the first study to examine CO2 efflux from marine aquaculture/shellfish ponds and in relation to land-use change from mangrove forests in China. Light and dark sediment CO2 efflux from shellfish ponds averaged at 0.61 ± 0.07 and 0.90 ± 0.12 kg CO2 m−2 yr−1 (= 37.67 ± 4.89 and 56.0 ± 6.13 mmol m−2 d−1), respectively. The corresponding rates (−4.21 ± 4.54 and 41.01 ± 4.15 mmol m−2 d−1) from the adjacent mangrove forests that were devoid of aquaculture wastewater were lower, while those from the adjacent mangrove forests (3.48 ± 7.83 and 73.02 ± 5.76 mmol m−2 d−1)) receiving aquaculture wastewater markedly increased. These effluxes are significantly higher than those reported for mangrove forests to date, which is attributable to the high nutrient levels and the physical disturbance of the substrate associated with the aquaculture operation. A rise of 1 °C in the sediment temperature resulted in a 6.56% rise in CO2 released from the shellfish ponds. Combined with pond area data, the total CO2 released from shellfish ponds in 2019 was estimated to be ~12 times that in 1983. The total annual CO2 emission from shellfish ponds associated with mangrove conversion reached 2-5 Tg, offsetting the C storage by mangrove forests in China. These are significant environmental consequences rather than just a simple shift of land use. Around 30% higher CO2 emissions are expected from aquaculture ponds (including shellfish ponds) compared to shellfish ponds alone. Total annual CO2 emission from shellfish ponds will likely decrease to the level reported in early 1980 under the pond area-shrinking scenario, but it will be more than doubled under the business-as-usual scenario projected for 2050. This study highlights the necessity of curbing the expansion of aquaculture ponds in valuable coastal wetlands and increasing mangrove restoration to abandoned ponds.