In this study, based on seismic profiles, complemented with boreholes and well logs, two types of deltas are recognized in the Paleogene Qiongdongnan Basin, namely fan deltas and braided river deltas, and their temporal–spatial evolution characteristics and associated controlling factors are studied. The results show the following: (1) The base-level cycle and episodic rifting lead that the characteristics of the basin-marginal deltas vary among different system tracts, third-order sequences, and second-order sequences or rifting stages, i.e. the temporal evolution of the basin-marginal deltas. Among the different system tracts in each third-order sequences, the deltas in the lowstand system tracts are vertically thick with small horizontal extension, while those in the transgressive system tracts present retrogradation with limited vertical thickness and horizontal extension, and those in the highstand system tracts turn to present large extension and develop toplap points. Among the different third-order sequences in each rifting stage, the extension of the deltas presents a pattern “small-medium-large” from bottom to top. Among different rifting stages, the deltas also exhibit different characteristics in terms of extension and thickness, and even the type may change. (2) The paleogeomorphology controls the characteristics of the deltas in lateral space, which is mainly reflected by the fact that the gradient of the paleogeomorphology influences the scale and type of the deltas. This study will enhance our understanding of the relative influence of the controlling factors exerted on fan or braided river deltas, and aid in the exploration of the coal-measure source rocks in the Qiongdongnan Basin, which is a typical basin lacking boreholes, located in the South China Sea.