Aquaculture ponds are important contributors to greenhouse gas flux methane (CH_4), Taihu Lake region is one of the area with extensive aquaculture in China, while few direct flux measurements are available. Field measurements of CH_4 flux from the typical aquaculture wetland would help to minimize the uncertainty in estimation of greenhouse gases which emissions came from aquaculture wetlands worldwide. It also provides data support and basis for further accurate estimation of global greenhouse gas emission inventories. This study investigated the magnitude of CH_4 flux and the influencing factors from mixed fish and crab aquaculture ponds during March, 2016 and March, 2017 in the Taihu Lake. CH_4 flux was primarily pronounced during the waterlogging stages. The variations in CH_4 flux was significant related to sediment temperature (t), sediment dissolved organic carbon (DOC), and water dissolved oxygen concentration (DO). The annual CH_4 emission was 64.4 kg·hm~(-2) and 51.6 kg·hm~(-2) from the mixed fish aquaculture pond and the crab aquaculture pond, respectively. Significant differences in CH_4 flux between the mixed fish and crab aquaculture ponds were observed during the year (P<0.05). The CH_4 fluxes from the crab aquaculture pond were significantly affected by the aquatic vegetation. Compared to the treatment without aquatic, the annual CH_4 emission increased by 14.0% for the treatment with aquatic. Relative to the mixed fish aquaculture pond, the net economic benefit scaled global warming potential (NEB-scaled GWP-CH_4) significantly increased 80% from the crab aquaculture pond. Our results suggest that mixed fish and crab aquaculture ponds are important contributors to regional CH_4 emission into the atmosphere. Furthermore, we also suggest that the aquaculture pond type should be considered when evaluating regional GHG budgets.