Abstract: Compared with the simple basin and shallow zone of superimposed basin, the deep zone of superimposed basin is usually lack of vitrinite reflectance and other traditional paleothermometer, and has experienced several complicated thermal history. Because the early thermal recording was superimposed by later tectonic thermal events, single paleothermometer or single thermal history reconstruction model is difficult to apply. Unfolding itself first with methods of tectono-thermal reconstruction of sedimentary basins, the idea and method system of the tectono-thermal evolution reconstruction for the deep zone in superimposed basin are summarized according to the difficulties on reconstruction of multiple-episode thermal evolution history and taking the Sichuan Basin for an example. The thermal evolution research for deep zone of superimposed basin should adhere to three general principles: 1）The thermal history reconstruction should be based on the study of present geothermal field; 2）The thermal evolution of the basin should combine with regional tectonic evolution; 3）The geological, geophysical, and geochemical method are trinity. Moreover, the method system should combine forward with inverse modeling. Both the kinetics of lithospheric tectono-thermal evolution and the thermal evolution stage of paleothermometers are should considered.