Late Paleozoic strata in the southeastern Ordos Basin comprise targeted reservoirs for tight gas exploration. As a typical intracratonic basin, the Ordos Basin is characterized by low-accommodation space and a complex sediment infilling process, which attracts much attention. During the early Permian, the southeast area was fed by sediments from multiple sediment sources, which makes it difficult to identify the pinch-out of the sand bodies and reconstruct the sediment routing system. In this study, we reconstruct the paleo-topography of the late Paleozoic setting using high-resolution 2D and 3D seismic data. Thus, we identify two types of topography: the eastern block is presented as a semiclosed depression, and the western block is observed as a flat platform. Based on detrital zircon U–Pb data and heavy mineral assemblages, we reconstruct the provenance area and show that early Permian sediments originate from the northern margin of the Ordos Basin and from the northern Qinling orogenic belt in the south. By integrating the trace element contents, carbon and oxygen isotope data and sedimentary structure from core samples, we can observe the paleoenvironment and the corresponding facies associations in these blocks. The eastern block was infilled by a prograding delta; the western block was infilled by a tide-dominated delta or a wavy-dominated delta. By using stratigraphic forward modelling, we find that most sediments in the semiclosed setting are progradational and intensely interacted. In contrast, the sediments in the western block present an open setting, infilled and gently interacted. The fine-grained deposits were not easily preserved due to tidal or wave reworking processes in the shallow-water marine setting, and they were transported into deep-water areas. Furthermore, to explore the dominant factors in a pattern of fluvial–deltaic sand bodies formed in the low-accommodation basin, we rebuild the sediment routing system parameters and plot them on a bubble chart. According to the fitness between the depositional volume and the above parameters, we determine the key factors in the routing systems that formed. The results show that the sediment supply has a high relevance to the depositional volume in a semiclosed setting, such as the eastern block, while the terrain height may drive sedimentation in an open marine setting, such as the western block. We demonstrate that two different infill patterns and different sand-body stacking patterns with multiple sediment sources in a low-accommodation basin may serve as a model for similar settings.