Due to the influence of multiple tectonic movements in rift basins, the sequence and sedimentary filling modes of continental petroleum reservoirs are complex, which makes it difficult to establish isochronous stratigraphic frameworks and thus affects the accuracy of subsequent predictions of effective sand bodies. Taking the Guantao Formation of the Binxian uplift and the surrounding areas as an example, this study established the sequence stratigraphic framework of the Guantao Formation and discussed the controlling effect of sequence stratigraphy on sedimentary filling. According to a combination method of seismic data, well log data, the wavelet transform technique (WTT), and Integrated Prediction Error Filter Analysis (INPEFA) methods, the Guantao Formation in the study area can be divided into 1 long-term cycle (LNG), 4 mid-term cycles (MNG1–MNG4, from bottom to top), and 11 short-term cycles (SNG1–SNG11, from bottom to top). Based on comprehensive analysis of geological and seismic data, three sedimentary facies can be classified: alluvial fan facies, braided fluvial facies, and meandering fluvial facies. The sequence stratigraphic style of the study area has a significant controlling effect on sedimentation and sand body distribution. Different levels of cycles have different impacts on sedimentary facies/microfacies types, the development degree of each sedimentary microfacies, and sand body distribution. The long-term cycle controls the distribution of sedimentary facies, while the mid-term and short-term cycles control the distribution of sedimentary microfacies. The bottom interface of the Guantao Formation (T1) served as the dominant migration channel in the study area, connecting the reservoir and source rocks. When the base-level was in the low stage (MNG1), a large amount of sand bodies developed, forming favorable reservoirs for petroleum. The interlayers at the top of the long- and mid-term cycles served as seal layers to prevent oil and gas from escaping. The MNG1 cycle has a good combination of reservoir and seal, resulting in the accumulation of oil and gas in the MNG1 strata, which became the main oil- and gas-producing layer in the area. These study results can provide effective guidance for future prediction of the distribution of sand bodies and high-quality reservoirs.