The sensitive online detection technique for heavy metal ions present in ocean, while effectively eliminating the interference of other chemicals, has been lacking at the present time. We found that the interfacial barrier of ZnO/rGO/PPy heterostructure had powerful physical effects on electrochemistry, and the Schottky barrier driven electrochemical detection was further developed. As based on the interfacial physical barrier, it could avoid the existing problem of the traditional electrochemical sensing mechanism and apply in more interfering environment. The sensitive detection of trace mercury ion (Hg2+) in actual seawater was achieved by employing the ZnO/rGO/PPy heterostructure. The interfacial barrier effect provides a chance to develop sensors used in more interfering environment.