The Neoproterozoic–Cambrian transition was a key time interval in the history of the Earth, especially for variations in oceanic and atmospheric chemical composition. However, two conflicting views exist concerning the nature of ocean chemistry across the Precambrian–Cambrian boundary. Abundant geochemical evidence suggests that oceanic basins were fully oxygenated by the late Ediacaran, while other studies provide seemingly conflicting evidence for anoxic deep waters, with ferruginous conditions [Fe(II)-enriched] persisting into the Cambrian. Here, two early Cambrian sedimentary platform and shelf-slope sections in South China were investigated to trace early Cambrian ocean chemistry from Mo isotopes. The results reveal that early Cambrian sediments deposited under oxic to anoxic/euxinic conditions have δ98/95Mo values ranging from −0.28‰ to 2.29‰, which suggests that early Cambrian seawater may have had δ98/95Mo values of at least 2.29‰, similar to modern oceans. The heaviest and relatively homogeneous δ98/95Mo values were recorded in siltstone samples formed under completely oxic conditions, which is considered that Mn oxide-free shuttling was responsible for such heavy δ98/95Mo value. Further, combined with Fe species data and the accumulation extent of Mo and U, the variation of δ98/95Mo values in the two studied sections demonstrate a redox-stratified ocean with completely oxic shallow water and predominantly anoxic (even euxinic) deeper water having developed early on, which eventually became completely oxygenated. This suggests that oceanic circulation at the time became reorganized, and such changes in oceanic chemistry may have been responsible for triggering the “Cambrian Explosion” of biological diversity.