The relationship between deposition and tectonics of sedimentary basins has been a significant subject in recent years. Using typical rift basins such as the Nanpu Sag as an example, combined with the analysis of the tectonics-palaeogeomorphology of basins, we undertook a detailed study of the differences of the third-order sequences in different basins, the combination of depositional systems within the sequence framework and the distribution of depocenters and subsidence centers. Our results revealed a significant relationship between the tectonics-palaeogeomorphology of rift basins and the filling styles of sedimentary sequences. The basin structure plays a primary role in controlling the development of the third-order sequences and the boundary of these sequences is easily formed in basins with gentle slopes, shallow water and a small area. The characteristics of the tectonics-palaeogeomorphology of rift basins are dominated by half-grabens of extensional faults, which affect the temporal and spatial combination of sedimentary systems within the sequences as well as the distribution of depocenters and subsidence centers. Based on the development rules of the faults dominating the half-grabens of extensional faults, rift basins are classified into two types: the single fault segmented-linkage type and the multi-fault combination type. The main controlling factors of the temporal and spatial combination of sedimentary systems and the distribution of depocenters and subsidence centers in different basins are different. The characteristics of early segmentation and later linkage of the faults play a critical role in controlling the sedimentary system combination within the sequence framework and the temporal and spatial differences of depocenters and subsidence centers of the single fault segmented-linkage rift basins, while the differences in fault activities are the dominating factors of the multi-fault combination rift basins.