The Sichuan–Yunnan–Guizhou Pb–Zn metallogenic province in the western Yangtze Block, southwest China, contains more than four hundred Pb–Zn deposits with more than 200 million tons of Pb–Zn ores at mean grades of 5 wt.% Pb and 10 wt.% Zn. These deposits are hosted in Sinian (Ediacaran) to Permian carbonate rocks and are structurally controlled by thrust fault–fold structures, and are spatially associated with the late Permian ~ 260 Ma Emeishan flood basalts. Two representative low temperature hydrothermal Pb–Zn sulfide deposits, the Tianqiao and Banbanqiao deposits in the southeastern part of the Sichuan–Yunnan–Guizhou Pb–Zn metallogenic province are selected for Zn–S–Pb isotopic analyses. Sphalerite from the Tianqiao deposit has δ⁶⁶Zn values ranging from − 0.26 to + 0.58‰ relative to the JMC 3–0749L zinc isotope standard, whereas δ⁶⁶Zn values of sphalerite from the Banbanqiao deposit range from + 0.07 to + 0.71‰. The zinc isotopic composition of sphalerite from both deposits increase from early to final mineralization stage. In addition, sphalerite from the center (near to bottom) part of the No. 1 ore body in the Tianqiao deposit has lower δ⁶⁶Zn values (− 0.01 to + 0.43‰) than those (+ 0.11 to + 0.57‰) in the periphery (near to top). Sinian to Permian sedimentary rocks and Permian Emeishan flood basalts, the potential zinc metal source rocks, have δ⁶⁶Zn values range from − 0.24 to + 0.17‰ and from + 0.32 to + 0.44‰, respectively. The majority of the hydrothermal sphalerite has heavier zinc isotope than the country rocks, precluding the mixing of multiple zinc sources as the key factor controlling the spatial and temporal variations of zinc isotope. Therefore, the increased δ⁶⁶Zn values from the early to late stage and from the center to top could be due to kinetic Raleigh fractionation. Sphalerite from the Tianqiao and Banbanqiao deposits has δ³⁴S values ranging from + 10.9 to + 14.8‰ and from + 3.9 to + 9.0‰, respectively, lower than Cambrian to Permian marine sulfates (+ 15 to + 35‰) and sulfate-bearing evaporates (+ 15 to + 28‰) in the Devonian to Permian carbonate host rocks. Sulfur of the Pb–Zn ores from both deposits is interpreted as the result of thermal chemical sulfate reduction of evaporates in the sedimentary rocks, most likely the host rocks. Sphalerite from the Tianqiao deposit has Pb isotope similar to that of age-corrected Devonian to Permian carbonate host rocks, whereas sphalerite from the Banbanqiao deposit has Pb isotope similar to that of age-corrected underlying Precambrian basement rocks. Therefore, at least lead in the Tianqiao and Banbanqiao deposits was mainly originated from the host rocks and the underlying basements, respectively. Zn–S–Pb isotopic studies of sphalerite from both deposits indicate that sources of metals and sulfur in the hydrothermal fluid for the Tianqiao deposit are the Paleozoic carbonate host rocks, whereas for the Banbanqiao deposit the sources are the Precambrian basements and the Paleozoic carbonate host rocks, respectively.