During the late Silurian – Early Devonian there were significant changes in the biosphere and environment. However, there are few integrated studies of carbon and sulfur cycling in the Qujing Basin, in South China, which has extremely well-preserved sarcopterygian fossils. Here we report C-isotopic data of organic carbon (δ13Corg) and multiple S-isotopes of pyrite (δ34S and Δ33S) from two sections in the Qujing Basin. Our δ13Corg data show an increase of ~4‰ near the Silurian-Devonian boundary which can be correlated globally. We suggest that this rise in δ13Corg near the Silurian-Devonian boundary may have resulted from the weathering of the 13C-enriched carbonate platform, rather than from oceanic anoxia. This interpretation may explain why there is little evidence of a mass extinction near the Silurian-Devonian boundary in the Qujing Basin. Our S-isotopic data show positive δ34S values with either positive or negative Δ33S values, and most of the δ34S and Δ33S data can be explained by microbial sulfate reduction and Rayleigh distillation processes. The S-isotopic data from both sections suggest that seawater sulfate concentrations were very low in the Qujing Basin during the late Silurian – Early Devonian.