Sedimentary rocks from the Ediacaran–Cambrian boundary record important biological, climatic and geotectonic changes during this time. To date, only few geochemical investigations on the upper Ediacaran – upper Cambrian rocks in the Tarim Basin have been carried out. Here, we report high-resolution δ13Ccarb records from the Penglaiba, the Wushi phosphorite and the Dongergou sections from Ediacaran–Cambrian Series 3 in the Keping area of the Tarim Basin. The sections display several obvious δ13Ccarb shifts; δ13Ccarb values increased from 3‰ to 6.7‰ across the Qigebulage Formation. Moreover, a negative δ13Ccarb shift across the Ediacaran–Cambrian boundary is apparent; δ13Ccarb values decreased to a minimum of −9.8‰ in the Wushi phosphorite section (−7.7‰ in Dongergou section and −5.4‰ in Penglaiba section), followed by a positive carbonate carbon isotopic excursion across the Yuertusi Formation into the middle of the overlying Xiaoerbulak Formation. Furthermore, more or less invariable positive δ13Ccarb values characterize the middle and upper Xiaoerbulak Formation. The most negative δ13Ccarb value (−14.3‰) occurred near the base of the Shayilik Formation, which is the absolute minimum value among the studied sections of the Cambrian Series 2 to Cambrian Series 3 transition in the world. The δ13C data from Keping, Tarim Basin are in good agreement with carbon isotope profiles recorded in South China, and these events may reflect the perturbation of the carbon cycle in the Tarim Basin during the Ediacaran–Cambrian and the Cambrian Series 2 – Cambrian Series 3 transitions.