Viewed from sedimentary records, the uplift and deformation in the southeastern margin of Sichuan basin occurred later than late Jurassic. Prior to this event, there existed a favorable petroleum geological conditions resulting in large scale hydrocarbon accumulation in this area. However, hydrocarbon accumulation was destroyed and adjusted by uplift and deformation of the sedimentary sequence. It is of great significance to determine the time limit of uplift and analyze its effect on hydrocarbon accumulation. 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 apatite track lengths are distributed mostly in the single peak form, with a few in the double-peak form. The mean track length is between 10 μm and 13 μm, and standard error is between 1.5 μm and 2.5 μm. The distribution characteristics of fission tracks suggest that the samples have experienced a slow cooling process. The thermal history simulation results show that all the samples have not experienced obvious subsidence since they entered the partial annealing zone. Almost all the samples have experienced three uplift periods, i.e., fast uplift in the early period, gentle uplift in the middle period and fast uplift in the late period, with the uplift time being different in different areas. The first uplift period in the southeastern margin of Sichuan basin occurred at about 90～60 Ma, and the arrival at the margin of the basin occurred at 40～35 Ma after northward transmission. Almost all of the samples experienced fast uplift events in late Cenozoic, and the time limit of them are within 10 Ma, with most of them being younger than 5 Ma and a few of them younger than 2 Ma. From the angle of plate tectonics, the uplift of this area in Himalayan period was related to the uplift of Tibet. 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.