The sequence stratigraphy framework of Paleogene of Qikou Sag has been built in this paper. The evolution law of episodic subsidence in Qikou Sag has been expounded, with the analysis of the characteristic of sequence thickness, as well as the study of consedimental tectonic activity, subsidence history, paleogeomorphology and the coupling relationship among them. The faults controlling action was the dominant mechanism during rifting stage I , as the depression was the dominant mechanism during rifting stage III, which embodies a process from intense disparity fault depression to integral subsidence. Meanwhile, under the control of regional faulting and later stage depression, subsidence rate centers and paleogeomorphic concave centers are always corresponding to the sequence thickness centers, and the changes of subsidence centers and paleogeomorphology concave centers are consistent with the migration of thickness centers, which presents the restriction, coupling and response among them and clarifies the law that tectonic activity controls the basin fill by means of controlling the subsidence rate and paleogeomorphology from contributing factor angle. On this basis, the dynamic evolution of the composite pattern of structure-subsidence-deposition in the fault controlling actic region during the three rifting stages and their petroleum geological significance has been discussed.