Freshwater lakes are hotspots in the global carbon cycle and significant sources of surface carbon emissions. This study focuses on the satellite lakes within the Poyang Lake Basin, the largest throughflow freshwater lake in China. By integrating cavity ring-down spectroscopy, stable isotope analysis, and organic matter spectroscopic analysis, we systematically investigate the spatiotemporal characteristics, methane (CH4) prduction pathways, and key driving factors of carbon dioxide (CO2) and CH4 emissions under different hydrological conditions. The results reveal that carbon emission fluxes from the satellite lakes in the Poyang Lake Basin exhibit significant spatiotemporal heterogeneity driven primarily by hydrological conditions. The seasonal patterns of CO2 emission fluxes varied across lakes of different scales. Large and medium-sized lakes exhibited higher emissions during the wet season due to enhanced terrestrial inputs and heterotrophic respiration, with a mean of 13.68 ± 26.77 mmol m-2 d-1.Conversely, small lakes (<10 km2) displayed higher emissions during the dry season, with an average flux of 18.23 ± 28.72 mmol m-2 d-1. Hotspots of CO2 emission remained concentrated in river inlets and shallow zones, which are strongly influenced by terrestrial inputs, with peak fluxes reaching up to 127.80 mmol m-2 d-1 during the wet season. Concurrently, CH4 emissions were consistently higher during the wet season than the dry season across all lakes. This seasonal difference was particularly pronounced in medium-sized lakes, where the average flux increased from 0.07 ± 0.12 mmol m-2 d-1 in the dry season to 0.27 ± 0.23 mmol m-2 d-1 in the wet season; however, localized peak emissions in the dry season could reach as high as 2.6 mmol m-2d-1. Stable isotope analysis revealed a shift in methanogenic pathways from the wet to the dry season. The overall range of αC narrowed, with the maximum value decreasing from 1.07 to 1.05, indicating a transition from coexisting hydrogenotrophic and acetoclastic methanogenesis during the wet season to a predominance of acetoclastic methanogenesis during the dry season. Further analysis indicated that the primary drivers of CO2 emissions shifted from allochthonous inputs and respiration in the wet season to autochthonous photochemical and biological degradation in the dry season. Similarly, CH4 production transitioned from benthic methanogenesis fueled by allochthonous substrates to the decomposition of autochthonous matter in local microenvironments. These findings demonstrate that catchment processes significantly affect throughflow lakes carbon emissions, contributing to a deeper understanding of the dynamics of lake carbon cycling.