In the context of accelerated economic development, freshwater ecosystems are increasingly subject to the process of eutrophication, which has precipitated a series of ecological issues within aquatic environments, 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 frequently emphasize water quality improvement, yet research on the impact on greenhouse gas fluxes is lacking. This study investigated the restored and unrestored areas of Lake Xuanwu (Nanjing) 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 demonstrated 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 found to be significantly higher than those in the restored area. The CO2 diffusion flux in the restored area was consistently lower than that observed in the unrestored area across all seasons. The CH4 diffusion flux at the water-atmosphere interface in the unrestored area was found to be higher than that in the restored area in all seasons. Within the unrestored area, the phytoplankton biomass demonstrated a strong positive correlation with TP, pH, and Chl.a, and a strong negative correlation with nitrate nitrogen, dissolved inorganic carbon, etc. In the area that had been restored, there was a strong positive correlation between the submerged plant biomass and salinity and conductivity, and a negative correlation with ammonia nitrogen, phosphate, CO2 and CH4 fluxes. It is evident that ecological restoration has a multifaceted impact on the environment, including the enhancement of water quality in eutrophic shallow lakes and the reduction of carbon-containing greenhouse gas emissions. The objective of the present study is to provide scientific references for the purpose of improving the carbon sequestration and sink function of lakes.