In the Early Jurassic, a large-scale transgression occurred on the South China continental margin (SCCM), affected by the initiation of Paleo-Pacific subduction. This transgression significantly influenced the source areas and transport mode of Lower Jurassic sediments in the SCCM. This study discussed the differences in the major source areas among the western, central, and eastern SCCM and constructed a brief Lower Jurassic sediments transport process in the SCCM. To avoid the bias of detrital-zircon ages caused by variations in zircon fertility, we gathered 1802 whole-rock zirconium content values (ppm) from representative granites with different ages in the South China Craton. Based on mean Zr contents and statistical analyses, we divided these granitic rocks into three groups: Group A consists of Jurassic (200–145 Ma) and Neoproterozoic (900–700 Ma), Group B consists of Paleozoic (490–390 Ma) and Permian–Triassic (280–210 Ma), and Group C comprised Paleoproterozoic (2000–1700 Ma) and Neoarchean (2900–2500 Ma). This research assigned these groups zircon fertility factors (ZFF) of 1.0, 1.4, and 2.5, respectively. Subsequently, by studying corrected detrital zircon ages from Lower Jurassic sediments by ZFF, we found that the Yunkai Terrane and Hainan Island were primary source areas for the western SCCM. The Wuyi Terrane and Nanling Tectonic Belt provided abundant detrital materials for the eastern SCCM. It should be noted that the central SCCM was a vast shallow sea in the Early Jurassic due to the large-scale transgression. Thus, the coastal currents and drowned pre-Jurassic river valleys controlled sediment delivery to the central SCCM. Overall, the Lower Jurassic sediments distribution system in the SCCM was significantly affected by Paleo-Pacific subduction.