It is important to understand the role of Qinghai–Xizang Plateau thermokarst lakes in the global atmospheric methane (CH4) and carbon dioxide (CO2) budget. This study investigated the gas components and isotopic characteristics of bubble gas collected from six thermokarst lakes. The major gas component of the bubbles varied greatly among lakes and bubble sources. Nitrogen (N2), oxygen (O2) and carbon dioxide (CO2) were the predominant constituents of bubbles, but argon (Ar) and methane (CH4) were also present. The N2 was primarily atmospheric in origin, although in part likely originated in sediment organic matter. Isotopic analysis of CO2 and CH4 suggested that CO2 in the bubbles was a mixture of CO2 from decomposed lacustrine carbonate and oxidized organic mass, except for CO2 from organic mass oxidized in Bucha Lake. CH4 in bubbles primarily originated from thermogenic sources and old sediment organic matter.