The Emeishan continental flood basalt, which is widespread in Yunnan, Guizhou and Sichuan provinces of Southwest China, is the volcanic product of a Permian mantle plume, and native copper-chalcocite mineralization associated with the basalt is very common in the border area of Yunnan and Guizhou provinces. The mineralization occurred in the tuff intercalation and terrestrial sedimentary rock intercalation which were formed during the main period of basalt eruption. The orebodies are controlled by the stratigraphic position and faults. Metal ore minerals in the ores are mainly native copper, chalcocite and tenorite, with small amounts of chalcopyrite, bomite, pyrite and malachite, and sometimes with large amounts of bitumen, carbon and plant debris. Several decades of ore deposits are distributed in the neighboring areas of the two provinces, while most of them are small-scale deposits or only ore occurrences. By comparing the lead isotopic composition of the ores with that of the wall-rocks, cover and basement rocks of various periods, the source of copper in this type of ore deposits was studied in this paper. The results showed that: (1) The Pb isotopic composition of the ores from ten deposits is absolutely different from that of siliceous-argillaceus rocks of the Upper Permian Xuanwei Formation, limestones of the Lower Permian Series and Carboniferous, Cambrian sandstone-shale and recta-sedimentary rock and dolomite from the upper part of the Meso-Proterozoic Kunyang Group. This indicates that ore lead was derived neither from the cover rock nor from the basement rocks; (2) Although the Neo-Proterozoic Siman dolomite and silicalite, and dolomite in the lower part of the Kunyang Group are similar in Pb isotopic composition to the ores, lead and copper contents in these rocks are very low and they have not made great contributions to copper mineralization; (3) The ores have the same Pb isotopic composition as the basalt, the latter being enriched in copper. These facts indicate that lead and copper were derived from the basalt. According to the regional geological data and the geological-geochemical characteristics of the ore deposits, it is suggested that ore-forming materials were leached out from the basalt. The thickness and buried depth of the basalt and regional tectonic dynamics can affect the formation of large-scale copper deposits. Therefore, exploration for this type of ore deposits should be conducted in the areas from western Yunnan to western Sichuan, where there are developed basalts of great thickness, with extensive tectonic movement and magmatic activity.