The Permian global mass extinction events and the eruption of the Emeishan flood basalts in the Upper Yangtze region should display certain responses during the evolution of carbon isotope. In this paper, the Permian carbon isotopic evolution in the Upper Yangtze region is examined through systematic stratotype section sampling and determination of 13C in the northern Upper-Yangtze regions and Southern China. Additionally, the carbon isotopic evolution response characteristics of the geological events in the region are evaluated, comparing the sea-level changes in the Upper Yangtze region and the global sea-level change curves. Results of this study indicated that the carbon isotopic curves of the Permian in the Upper Yangtze region are characterized by higher background carbon-isotope baseline values, with three distinct negative excursions, which are located at the Middle–Late Permian boundary and the late period and end of the Late Permian. The three distinct negative excursions provide an insightful record of the global Permian mass extinction events and the eruption of the Emeishan flood basalts in the Upper Yangtze region. The first negative excursion at the Middle–Late Permian boundary reflected the eruption of the Emeishan flood basalts, a decrease in sea level, and biological extinction events of different genera in varying degrees. The second negative excursion in the Late Permian included a decrease in sea level and large-scale biological replacement events. The third negative excursion of the carbon isotope at the end of the Permian corresponded unusually to a rise rather than a decrease in sea level, and it revealed the largest biological mass extinction event in history.