The Carboniferous–Triassic period was an important stage of global sea–land transformation, with coal formation in the Carboniferous, biological extinction at the end of the Permian, and global drought in the Triassic. The MS-1 well in the Mosuowan High of the Junggar Basin is the deepest well drilled in Northwestern China. In this paper, we investigate the sedimentary environment and climate evolution of the Mosuowan area in the central Junggar Basin during the Late Carboniferous–Early Permian by the petrothermal, lipid biomarker, and isotopic composition of mud shale core samples, and explore the tectonic–climatic events and Central Asian orogenic belt evolution driving the sedimentary environment. The study shows that the organic matter from the Upper Carboniferous to the Lower Permian is at a mature stage, but biomarkers maintained the primary information although the organic matter was subjected to thermal evolution. In the late Carboniferous period (Tamugan Formation), the study area was a closed remnant sea with a relatively humid climate, triggering lush terrestrial vegetation and high organic carbon content in the sediments, which had the potential to evolve into natural gas. During the Xiazijie Formation of the Middle Permian, tectonic activity shifted to the subsidence period, and the salinity of the water decreased after a large input of fresh water. The lake basin area expanded, and the content of aquatic organisms continued to increase. As the Lower Permian stratigraphy is missing, this sea–land transition seems to jump. The low and upper Urho Formations of the Middle–Upper Permian are a deltaic foreland deposit, and geochemical indicators show an overall lake retreat process with a continuous increase in organic matter content of terrestrial origin. The lithologic assemblage of the Triassic Baikouquan Formation is braided river deltaic sedimentation with migration of deposition centers of the lake basin. In conclusion, the Late Carboniferous–Early Permian period was influenced by global changes, Paleo-Asian Ocean subduction, and continental splicing, which resulted in a continuous increase in terrestrial organic matter, water desalination, and oxidation-rich sediments in the Mosuowan region, but the P–T biological mass extinction event was not recorded.