Abundant bedded chert deposits occurred at the Ediacaran–Cambrian transition interval at the Yangtze Platform, South China. However, there is not a non-controversial and integrated model for the origin of these chert deposits from trace element patterns and oxygen isotopic evidence. To understand the origin and the oceanic environment of these chert deposits, we analyzed the Si isotopic composition, major and trace elements of chert samples from two stratigraphically correlated sections with a depositional age around 542 Ma. The relationship between Al₂O₃ content and Si isotopic values indicated three end-member sources of Si derivation. The most negative δ³⁰Si values (−0.3‰ to −0.5‰) reflect the silicon derived from hydrothermal fluids due to intense tectonic activity. The most positive δ³⁰Si values (up to +1.2‰) could reflect the increase of ³⁰Si in the hydrothermal fluid by precipitation, or the signature of seawater. The medium δ³⁰Si value (+0.2‰ to +0.7‰) could be interpreted as the mixing of the hydrothermal fluid and volcanic materials with negative δ³⁰Si and ambient seawater with positive δ³⁰Si. It is obvious that the injection of Si-rich hydrothermal fluid would affect the δ³⁰Si and trace element distribution of seawater. In addition, we estimated that the δ³⁰Si values of Ediacaran–Cambrian transitional seawater range from +2.2‰ to +3.5‰ based on assumed fractionation factors −2.3‰ < ɛ < −1.0‰ between precipitated Si in chert deposits and initial dissolved Si in seawater. According to Si isotopic composition and other geochemical evidence, we maintain that hydrothermal activity played an important role not only in the formation of bedded chert and polymetallic ore deposits, but also in the oceanic environment and concurrent evolution of life during Ediacaran–Cambrian transition interval.