River and stream sediments act as biogeochemical reactors for greenhouse gases, particularly methane. However, understanding how riverbed sediment properties influence river carbon emissions remains relatively unclear. The Liao River in northern China is a typical watershed with heterogeneous water and sediment sources, characterized by varying sediment properties. In this study, we surveyed CH4 and CO2 emissions from its mainstem and tributaries during flood and dry seasons. We found consistent seasonal patterns in CH4 and CO2 emissions, with peaks occurring during the flood season. The average CH4 and CO2 fluxes were 1.64 ± 1.80 mmol·m−2·d−1 and 59.66 ± 44.60 mmol·m−2·d−1, respectively. Notably, the percentage of sediment silt was significantly correlated with CH4 concentration and flux (R2 = 0.12−0.30, p < 0.05). Fine particles dominated the availability of sediment organic matter and redox conditions, which were related to riverine CH4 production and emissions. Structural equation modeling revealed that both grain size and the percentage of TOC (total organic carbon) directly influenced riverine CH4 and CO2 emissions. The organic content and redox conditions of the riverbed sediment collectively explained 65% of riverine CH4 emissions, while grain size composition indirectly controlled CH4 emissions by altering sediment substrate quality and redox conditions. In contrast, river CO2 emissions were only weakly dependent on anaerobic metabolism in riverbed sediments. These findings enhance our understanding of the sources and metabolic mechanisms of riverine CH4 and CO2 emissions and offer potential improvements for estimating carbon fluxes in regional or global riverine networks by considering riverbed sediment properties.