Inland aquaculture ponds in China collectively cover 2.57 million ha, so emissions of the greenhouse gases methane (CH4) and nitrous oxide (N2O) from these ponds may constitute a significant contribution to global warming. During 2016 and 2017, CH4 and N2O fluxes and a range of pond-water and sediment properties were measured in replicated (n = 4) “mixed-fish” and “crab” aquaculture ponds in southeast China. Annual CH4 and N2O emissions were 64.4 kg C ha−1 and 2.99 kg N ha−1, respectively, from the “mixed-fish” ponds, and 51.6 kg C ha−1 and 3.32 kg N ha−1, respectively, from the “crab” ponds. Emission differences between pond types were significant (p < 0.05) for both gases. CH4 fluxes from the “crab” ponds were significantly increased by the presence of aquatic vegetation, but N2O fluxes were not affected. Emissions of N2O were estimated to be 0.54% and 0.71% of the total nitrogen input (in the feed) for the “mixed-fish” and “crab” ponds, respectively. The net economic benefit-scaled sustained-flux global warming potential (NEB-scaled SGWP) of the “crab” ponds was 61.6% higher (p < 0.05) than that of the “mixed-fish” pond. Our CH4 and N2O emissions results suggest that aquaculture ponds can be important contributors to regional and national GHG inventories, with aquaculture type an important factor in total GHG impact. Further CH4 and N2O flux research is needed at aquaculture ponds across China to better establish the range of potential GHG impacts, and to confirm the importance of the influencing factors identified in this study.