The understanding of sublayer division and stratigraphic filling law is of great significance for the depiction of sedimentary paleotopography. The previous study of the cyclical stratigraphic correlation between the Liangshan Formation and the Qixia Formation was separated, which made it difficult to restore the conversion process between the coastal sedimentary system of the Liangshan Formation in the whole basin and the subsequent carbonate sedimentary platform, and hindered the understanding of the filling law of the Qixia Formation. In view of this, the Qixia Formation in the northwestern Sichuan Basin, which has rich field profiles and drilling data. Based on the geodetic logging wells, three high-precision gamma outcrops and core observation, the characteristics of the cyclic interface have been recognized, and the sublayer division and comparison of the system have been done. Then, the formation filling process have been determined. The conclusion shows that there is a layer filling feature of “baselap and topping” in the study area: the paleo-geomorphology of the Permian sedimentary deposits in the study area is basically flattened, and the initial sedimentary stage of the Liangshan-Qixia Formation is a gentle slope of the local secondary uplift and depression. The northern margin stratum of the Yangtze Platform continues to overtake the Zhuyuanba-Mineliang and Hannan paleo-continental belts in the early times. This position becomes the granular beach development zone under the background of gentle slopes. During the initial sedimentary period of the second member of the Qixia Formation, the sea-land pattern begins to transform, and the Zhongba-Shuangyushi-Shejianhe and to the east area are uplifted differently, also the secondary fracture begins to control the development of the granular beach. At the end of the sediment of the Qixia Formation, the Longmenshan piedmont zone and the Hannan underwater paleo-uplift are exposed to atmospheric freshwater with leaching and erosion on it. The relative highlands have suffered a certain degree of erosion, and there is a general cyclic lack in the drilling positions, such as Shuangyushi. Based on the above understanding, at this time, the boundary between the first member of Qixia Formation and the second member of Qixia Formation was selected as the base level to restore the paleo-geomorphology before the sediment of Qixia Formation and the paleo-geomorphology at the top of the second member of Qixia Formation using the impression method and the residual thickness method comprehensively.