Recently, the research of the internet of vessels system is a hotspot in the marine engineering area. In this article, the Internet of Vessels based on Beidou satellite navigation system (IoV-BDS) architecture is proposed for marine cold chain transportation monitoring and scheduling. An improved communication method using Beidou short-message communication (SMC) is designed to ensure the reliability of ship-shore data transmission. Additionally, based on the IoV-BDS, we proposed a novel route scheduling optimization model which considers the key costs for marine cold chain transportation, such as fuel, catches damage, and refrigeration energy consumption, and designed a speed selection mechanism. Furthermore, an improved ant colony optimization (IACO) algorithm was utilized to optimize the whole fleet transportation routes, which takes advantage of the A-star algorithm to speed up the convergence of ant colony algorithm (ACO), a novel state transition rule was used to prevent falling into a locally optimal solution. The applicability of IoV-BDS was verified by the shipboard data acquisition and Beidou SMC experiments. The performance evaluation and analysis of route optimization schemes were presented by simulations and comparison with other schemes. The results demonstrated the benefit of our proposed schemes, in terms of solution quality and convergence of the algorithm.INDEX TERMS IoV, Beidou SMC, cold chain, route optimization, refrigerator ship.