The Ediacaran–Cambrian transition period was a critical time interval for the environmental fluctuations and organismal evolution in geological history, popularly known as the “Cambrian Explosion”. The diagenetic mechanism of the widely developed Liuchapo bedded cherts in South China remain unclear and controversial during this critical time interval. To address this, we examined silicon and oxygen isotopes, as well as major and trace elements in the Liuchapo cherts from three wells developed from slope to basin facies in South China. Results reveal that the bedded cherts from the three wells were affected by episodic hydrothermal activity, and the percentage of hydrothermal fluids is highest in the Xc1 well and lowest in the Xb1 well. The paleo-seawater temperature, calculated from chert oxygen isotope values, present a gradual increasing trend from shallow- to deep- areas in South China from 542 to 526 Ma. Redox proxies indicate that the water column of the Xa1 and Xc1 wells were dominated by suboxic condition, while those of the Xb1 well was mainly in oxic conditions. There should exist an oxygen minimum zone (OMZ) during the shelf and slope transition. A suitable temperature and oxic environment are conducive to biological reproduction, which is consistent with higher primary productivity and abundant acritarch fossils in the Xb1 well. Silicon isotope values range from −0.6 ‰ to 1.2 ‰ in the three wells. The diagenetic origin of the Xa1, Xb1, and Xc1 wells was the consequence of the mixture of hydrothermal fluid and seawater, biological activity, and direct hydrothermal precipitation, respectively. Due to the redox condition and seawater temperature variation, silica-secreting organisms should be relatively limited. The episodic hydrothermal fluid, biological activity, and replacement of precursor rock may jointly affect the formation of the Liuchapo bedded cherts during the Ediacaran–Cambrian transition.