According to the aquatic trace identity in the existing regulatory system, a certification and traceability regulatory system based on USB Key was designed. Firstly, several authentication technologies were analyzed focusing on the advantages and disadvantages. Secondly, the key part of USB Key hardware circuit, software system and the certification process of USB Key aquatic products enterprises were designed to solve the security issues of aquatic information transmission. Finally, the aquatic product enterprise certification and traceability monitoring platform was applied in Jiangsu province. The results showed that the regulatory system was convenient, safety, stable and reliable. It can realize the origin of quasi-out, market access, business certification and real-time monitoring of aquatic enterprise governance traceability system.