As the economy rapidly develops, freshwater ecosystems suffer from eutrophication, leading to a series of aquatic ecological issues, including water quality deterioration and a decline in biodiversity. The most critical step in the ecological restoration of eutrophic shallow lakes is to achieve the transition of primary producers from phytoplankton to submerged macrophytes. Current ecological restoration projects of lakes often emphasize water quality improvement but lack research on the impact on greenhouse gas fluxes. This study investigated the restored and unrestored areas of Lake Xuanwu to compare the physicochemical parameters of the water and the carbon dioxide (CO2) and methane (CH4) fluxes at the water-atmosphere interface between the two areas. The results show that the concentration of chlorophyll a (Chl a) in the unrestored area was significantly higher than that in the restored area in all four seasons, reaching up to five times as much in the summer. The concentrations of total nitrogen (TN) and phosphorus (TP) in the unrestored area were also significantly higher than those in the restored area. The CO2 diffusion flux in the restored area was much lower than that in the unrestored area in all seasons. The CH4 diffusion flux at the water-atmosphere interface in the unrestored area was higher than that in the restored area in all seasons. Within the unrestored area, the phytoplankton biomass has a strong positive correlation with TP, pH, and Chl a, and a strong negative correlation with NO3--N, DIC, etc. In the restored area, the submerged plant biomass has a strong but non-significantly positive correlation with salinity and conductivity, and a negative correlation with NH4+-N, PO43--P, CO2 and CH4 fluxes. Overall, ecological restoration can effectively inhibit the rapid growth and reproduction of phytoplankton by restoring submerged macrophytes, improve the water quality of eutrophic shallow lakes, and reduce the flux of carbon-containing greenhouse gases by increasing the concentration of dissolved oxygen in water and sediment. This study will provide scientific references for improving the carbon sequestration and sink function of lake.