As the main solid waste disposal method in China, landfill sites are considerable sources of methane (CH4) and carbon dioxide (CO2). This study characterized the seasonal variation of CH4 and CO2 effluxes at a large and well-managed final covered landfill site in China. A three-year monitoring program was conducted. There were two different seasonal variation patterns for hotspot and non-hotspot’ CH4 and CO2 effluxes. For non-hotspots, the CH4 and CO2 effluxes' seasonal variations were mainly affected by the seasonal change of the landfill's cover soil respiration activity, particularly the CH4 oxidation capability. CH4 had a higher efflux in winter; in other seasons, the CH4 efflux fluctuated around 0; the CO2 effluxes were (1) increased in spring and peaked in summer or early autumn; (2) then, they decreased to a minimum value in late autumn or early winter; and (3) fluctuated with the CH4 efflux in winter. The CH4 emissions in winter account for 60.4–84.4% of the all year outputs. For the hotspots', the CH4 and CO2 effluxes seasonal variations were mainly determined by the seasonal change of the landfill cover's soil gas permeability. The ratio of CH4 emissions in winter to the all year outputs range from 17.4 to 68.7%.