The late Permian (Lopingian) was a crucial climate transition period from the late Paleozoic Ice Age to the early Triassic of exceptionally high temperatures. However, the origins of the third-order sea-level changes during the Lopingian Epoch remain unclear. Here, we presented astronomically calibrated gamma-ray (GR) log and non-U GR (computed gamma ray or CGR) curves from the clastic and carbonate successions of well GFD-1 in the Pingle Depression of South China for studying the sea-level oscillations during the Lopingian. Spectral analyses of the 405 kyr-calibrated GR and CGR time data revealed periodicities close to about 405, about 100, about 44.2, about 35.1, about 21, and about 17.5 kyr, supporting the existence of Milankovitch forcing in the sedimentary records. A high-resolution astronomical time scale and high-resolution sedimentation rate curve of the Lopingian from well GFD-1 were constructed by cyclostratigraphic analysis. The eccentricity and obliquity amplitude modulation cycles suggested long periodicities of about 2.4 and about 1.2 myr, respectively. In the Wuchiapingian greenhouse of the Lopingian, the about 2.4 myr eccentricity oscillation controlled ‘weak’ glacio-eustasy and/or aquifer eustatic changes related to the global third-order sea-level changes and that a lowstand (W2) was initiated by an eccentricity oscillation minimum. In contrast, during the Changhsingian, which exhibited a cooling event, an about 1.2 myr obliquity cycle was probably strong, with the sea-level records highlighting the link between the ‘icehouse’ sea-level lowering (C2 and C1) and the obliquity nodes. Moreover, dynamic sedimentary noise model as an indicator of sea-level showed local third-order sea-level variations, the coevolution trends in the orbital power, global and local sea-level changes, and sedimentation rate had significant implications for establishing the global nature and synchronicity of these million-year-scale eustatic records and reconstructing the temporal depositional history at a regional scale. In addition, the volcanism and tectonism that continued into the early-middle Wuchiapingian probably led to a series of climate changes that drove the hydrological cycles not paced by the Milankovitch cycles.