The end-Devonian mass extinction (similar to 359 Ma) substantially impacted marine ecosystems and shaped the roots of modern vertebrate biodiversity. Although multiple hypotheses have been proposed, no consensus has been reached about the mechanism inducing this extinction event. In this study, I/Ca ratio of carbonate was used to unravel the changes in local oxygen content of the upper water column during this critical interval. The Devonian-Carboniferous boundary was recorded in two shallow water carbonate sections in south China. I/Ca values at both locations show a clear decline in the Middle and Upper Siphonodella praesulcata conodont zones, which coincides with a positive shift in carbonate carbon isotope composition and a negative shift in nitrogen isotope composition. These results suggest that deoxygenation was intensified during this critical interval, which likely influenced shallow water habitats, lending support to the notion that oxygen deficiency likely was a direct mechanism impacting the end-Devonian mass extinction.