Due to limited communication, computing resources, and unstable environments, traditional cold chain traceability systems are difficult to apply directly to marine cold chain traceability scenarios. Motivated by these challenges, we construct an improved blockchain-based cold chain traceability system for marine fishery vessels. Firstly, an Internet of Vessels system based on the Iridium Satellites (IoV-IMS) is proposed for marine cold chain monitoring. Aiming at the problems of low throughput, long transaction latency, and high communication overhead in traditional cold chain traceability systems, based on the Practical Byzantine Fault Tolerance (PBFT) consensus algorithm, a Node-grouped and Reputation-evaluated PBFT (NR-PBFT) is proposed to improve the reliability and robustness of blockchain system. In NR-PBFT, an improved node grouping scheme is designed, which introduces a consistent hashing algorithm to divide nodes into consensus and candidate sets, reducing the number of nodes participating in the consensus process, to lower communication overhead and transaction latency. Then, a reputation evaluation model is proposed to improve the node selection mechanism of NR-PBFT. It enhances the enthusiasm of nodes to participate in consensus, which considers the distance between fishery vessels, data size, and refrigeration temperature factors of nodes to increase throughput. Finally, we carried out experiments on marine fishery vessels, and the effectiveness of the cold chain traceability system and NR-PBFT were verified. Compared with PBFT, the transaction latency of NR-PBFT shortened by 81.92%, the throughput increased by 84.21%, and the communication overhead decreased by 89.4%.