The Lomagundi (-Jatuli) event, characterized by extremely high positive global inorganic carbon isotope excursion at about 2.2 billion years ago, is pivotal in investigating the causes and consequences of great oxygenation event, inventory and sequestration of carbon on the Earth's surface, evolution of life, and more profoundly tectonic control on Earth's environment. However, the reasons that caused the isotopic excursion are not resolved yet. Herein, we report the discovery of meta-carbonate rocks with distinct positive carbon isotopic excursion from the Paleoproterozoic continental collision zone of the Kongling Complex, South China Craton. The δ13CV-PDB values for meta-carbonate rocks show positive values in the range from +5.5‰ to +11.6‰, whereas the δ13CV-PDB values of associated graphite deposits range from −25.8‰ to −9.5‰. Zircon U-Pb-Hf isotopes from zircon-bearing meta-carbonate sample yielded weighted average 207Pb/206Pb age of 2001.3 ± 9.5 Ma, with corresponding εHf(t) range from −7.05 to −3.16, comparable to the values of local 2.9–2.6 Ga basement rocks. Geochemical characteristics of meta-carbonate rocks, such as their rare earth element patterns and the trace element parameters of La, Ce, Eu, and Gd anomalies and Y/Ho ratio, suggest that the carbonate deposition took place in passive continental margin in association with large volumes of organic carbon. The extensive graphite deposits from Kongling Complex in South China Craton, their equivalents in the North China Craton and elsewhere across the globe prove that the burial of 12C-enriched organic carbon has eventually resulted in the global enrichment of 13C in the atmospheric CO2, which is recorded in the marine carbonate rocks. Isotopic mass balance estimates indicate that more than half of the organic carbon was buried during the oceanic closure. Hence, the observed global shift could be directly related to the continent collision event in greater China, thus resolving the long-standing paradox of the Lomagundi global positive carbon isotope excursion. Moreover, the present results suggest that orogenesis play a significant role in sequestration of carbon into the continental crust.