Riverine carbon is an important component of the global carbon cycle, and also provides insights into various natural processes and anthropogenic activities in the catchment. Cascade reservoirs seriously alter the natural state and biogeochemical cycles of rivers, but their effects on the carbon migration and transformation processes of rivers in alpine regions have not been fully investigated. In this study, the natural river section of the Lancang River and its downstream cascade reservoirs were selected to investigate the basic physical and chemical parameters of the river water, as well as the diel variations of riverine carbon contents and stable carbon isotopes. The aim was to investigate the migration and transformation processes of riverine carbon in the natural channel-cascade reservoirs continuum and to explore the influence of cascade reservoirs on carbon cycling through a comparative analysis. The results indicated that the particulate organic carbon content in the reservoir's water column was significantly lower than that in the natural river channel, reflecting the substantial trapping effect of the cascade reservoirs on particulate matter, with 98% of suspended solids being retained. The concentrations and fluxes of dissolved inorganic carbon and dissolved organic carbon exhibited no significant variations between the natural river channel and the reservoir sections, indicating that the cascade reservoirs had a minimal influence on the dissolved substances in the river. However, the partial pressure of carbon dioxide (pCO₂) in the water exhibited a decreasing trend from the natural river channel (average 689 μatm) to the reservoir area (average 587 μatm), with a more pronounced decline during the winter season. No significant diel variations were observed in the physicochemical parameters, carbon concentrations, or carbon isotope compositions of the water bodies at the Liutongjiang hydrologic station and the Gongguoqiao Reservoir. Moreover, there was no synergistic change between dissolved oxygen and pCO₂, indicating that aquatic photosynthesis within the river was weak. Stable carbon isotope data revealing alterations in carbon sources and carbon fluxes suggested that a substantial amount of riverine organic carbon was sequestered at the bottom of the reservoir. This weakened the internal oxidation were decomposition processes of organic carbon, leading to a decrease in pCO₂ in the surface waters of the reservoir. The low nutrient content, short reservoir age and frequent flow regulation were the primary factors contributing to the weak aquatic photosynthesis in the reservoir and its limited impact on river chemistry and the carbon cycle. Overall, the cascade reservoirs in the Lancang River basin had resulted in a significant increase in the deposition of riverine organic carbon with a considerable reduction in CO₂ outgassing, thus exhibiting a net carbon sink effect.