Thermokarst lakes are widely distributed on the Qinghai-Tibetan Plateau (QTP), which accounts for 8% of the global permafrost area. These lakes probably promote organic matter biodegradation and thus accelerate the emission of carbon-based greenhouse gases. However, little is known about greenhouse gas concentrations and their stable isotopes characteristics of these lakes. In this study, we measured the concentrations of dissolved organic carbon (DOC), dissolved CO2 and CH4, as well as the distribution of δ13CCO2, δ13CCH4, and δ13COM (organic matter) of lake sediments in thermokarst lakes on the QTP. Results showed that the OM of the lake sediments was highly decomposed. The concentrations of DOC, CO2 and CH4 in the lake water on the QTP were 1.2–49.6 mg L–1, 3.6–45.0 μmol L–1 and 0.28–3.0 μmol L–1, respectively. The highest CO2 and CH4 concentrations were recorded in July while the lowest values in September, which suggested that temperature had an effect on greenhouse gas production, although this pattern may also relate to thermal stratification of the water column. The results implied that thermokast lakes should be paid more attention to regarding carbon cycle and greenhouse gas emissions on the QTP.