Peatlands in Eurasian permafrost regions are among the world’s most important soil carbon reservoirs and may strongly influence future climate through carbon release. Runoff-mediated dissolved carbon export represents a critical carbon-loss pathway in permafrost peatlands, yet observations from the southern margin of Eurasian permafrost remain scarce. Here, we investigated dissolved carbon export from two differently sized permafrost peatland catchments in the Greater Khingan Mountains, northeastern China. We estimated dissolved organic carbon (DOC) and dissolved inorganic carbon (DIC) export fluxes and evaluated hydrological controls on dissolved carbon dynamics using three fluorescence indices. DOC and DIC concentrations were closely coupled with discharge during seasonal hydrological fluctuations, indicating that runoff dynamics were the primary driver of dissolved carbon export. During the growing season, the Fukuqi River exported 703.84 t total dissolved carbon, equivalent to approximately 20% of peatland net ecosystem exchange. Hydrological processes regulated not only dissolved carbon fluxes and the relative contributions of DOC and DIC, but also DOC chemical characteristics. Flood-peak flows promoted the export of more humified DOC, characterized by higher humification index and lower fluorescence index and freshness index, whereas baseflow showed the opposite pattern. The vertical organic–mineral stratification of peatland soils, with contrasting hydraulic transmissivity and dissolved-carbon production potential, directly governed temporal variations in discharge and dissolved carbon concentrations. Active-layer deepening may increase runoff contributions from deeper mineral soils, thereby increasing the DIC fraction while reducing DOC concentration and the degree of humification. Fluorescence indices were consistently correlated with discharge across both catchments, suggesting their potential as robust indicators of hydrological processes. Overall, these findings highlight runoff-mediated dissolved carbon export as an underrepresented carbon-loss pathway and suggest that permafrost degradation will reshape both the magnitude and chemical composition of dissolved carbon exports under future warming.