Carbon emission from reservoirs is considered to tarnish the green credentials of hydropower and has been extensively studied in single reservoirs. However, it remains unclear how carbon emission differs in cascade reservoirs and the mechanism behind the differences. In this study, carbon dioxide (CO2) and methane (CH4) emissions from cascade hydropower reservoirs were measured in the Lancang River, the Chinese section of the Mekong River. Our results demonstrate that carbon emissions from the river were increased by dam construction but exhibited spatial heterogeneity among cascade reservoirs. The first, most upstream, reservoir acted as the hotspot of CH4 and CO2 emissions, which were 13.1 and 1.7 times higher than those in downstream reservoirs, respectively. Similarly, the CH4/CO2 ratio of 0.023 in the first reservoir was higher than the others and made a greater contribution to the global warming effects of the cascade reservoirs. The sediment organic carbon in downstream reservoirs was negatively correlated with reservoir age (r2 = 0.993) and decreased at a rate of 0.389 mg g-1 yr-1, suggesting a potential decrease of carbon emission in the future. This study adds to our understanding of carbon emissions from cascade reservoirs and helps to screen effective strategies for future mitigation of the global warming effects from cascade hydropower systems.