Apatite fission track analysis(AFTA) and kinetic model of vitrinite reflectance(Ro) are applied to be the paleogeothermometers to analyse the thermal-tectonic evolution of the Western Qaidam Basin. By the modeling of thermal history from 16 wells, the thermal evolution status since the Tertiary time in this area was obtained. The thermal gradient decreased from the Tertiary time, but changed a little during the Quaternary. However, heat flow evolution during the Cenozoic time is special with that of thermal gradient. Heat flow increased gradually from Tertiary, which is correspond to the structural evolution by the erosion of strata. This study is the first time to analyse, systematically, heat flow evolution of the Qaidam Basin, which will be useful to the hydrocarbon resources assessment in the basin.