Evaluating the distribution and sea-air fluxes of dissolved methane (CH₄) in mariculture areas is important for understanding how aquaculture contributes to regional CH₄ emissions into the atmosphere. Seasonal field surveys conducted in 2023 were used to analyze the temporal and spatial variation of CH₄ concentrations in surface water and CH₄ air-sea flux in a typical aquaculture system in Sansha Bay, Fujian Province. The results showed that dissolved CH₄ concentrations ranged from 9.91 to 609.22 nmol/L, with corresponding air-sea fluxes between 3.46 to 1 188.15 μmol/ (m²·d). Temporally, the CH₄ air-sea fluxes were higher in summer and autumn compared to spring and winter. Spatially, CH₄ concentrations and air-sea fluxes decreased consistently from the estuary to the bay mouth, with the highest values in the estuarine aquaculture area and the lowest in the bay mouth aquaculture area. Correlation analysis showed that aquacultural activities and terrestrial runoff inputs contributed to the spatiotemporal distribution of CH₄ concentrations within the bay. In the macroalgae cultivation zones, CH₄ production and emissions during farming periods were significantly lower than during non-farming periods. Additionally, the residual feed and feces generated by fish in cages may result in increased CH₄ emissions. Notably, CH₄ emissions peaked in summer, due to enhanced aquaculture activities and runoff inputs during the wet season. Future work should focus on investigating CH₄ air-sea fluxes in mariculture areas to provide scientific support for CH₄ control and emission reduction in aquaculture.