Viewed from sedimentary records, the uplift and deformation in the southeastern margin of Sichuan Basin occurred later than Late Jurassic. Based on apatite fission track analysis of eight samples from different strata in the southeastern margin of Sichuan basin, the authors confirmed the Mesozoic-Cenozoic uplifting time limit and discussed its tectonic and petroleum geological significance. The thermal history simulation results show that all the samples have not experienced obvious subsidence since they entered the partial annealing zone. From the angel of petroleum geology, the intense uplifting in the southeastern margin of Sichuan Basin might have on the one hand destroyed the existent gas accumulations but on the other hand created favorable conditions for the formation of fractured gas accumulations and water-soluble gas accumulations.