Aiming to guarantee the quality and safety of aquatic product and the realization of its traceability system, the production, processing, logistics and vendition sections of the whole aquatic product industry chain and existing quality safety problems in China are demonstrated and analyzed in this paper with the perspective of the aquaculture industry chain. Furthermore, an IoT-based aquaculture industry chain traceability system and its application in all sections of the industry chain are proposed by means of introducing the concept and technology of the Internet of Things (IoT) which includes Radio Frequency Identification (RFID), 2D bar code, Global Positioning System (GPS), Geographic Information System (GIS), etc. In addition, the implementation methods in every sector of the whole aquatic product industry chain are analyzed. On the basis of the above content, an enterprise-government-consumer-oriented governmental aquatic product industry chain tracking and supervision cloud service is designed while a dynamic tracking mechanism of aquaculture product based on EPC and RFID is presented. As an illustration, the specimens of tracking information and EPC coding samples of aquatic product are designed, which drives the realization of the static tracing and dynamic tracking for the aquatic product industry chain in the whole time space. As the application and practice, Eriocheir sinensis is taken as the object of study and the idea and methods have been eventually applied into practice for the Shanghai-Taiwan Eriocheir sinensis transmission commission by the construction of a juvenile crab quality dynamic whole-process traceability system, which assisted 255 Taiwan raisers to track and release over 0.7 million Eriocheir sinensis into ponds.