Eliminating AIS blind spots and weak areas, and expanding the coverage of AIS shore-based systems is an effective means to enhance the perception ability of maritime vessels. However, due to limitations in communication infrastructure, the site selection of AIS base stations is greatly restricted. Utilizing the Beidou-3 short message communication system can solve the problem of backhauling AIS data within AIS signal coverage blind spots in the absence of communication support conditions. Due to the communication capacity limitations of Beidou-3, there is a significant transmission bottleneck when Beidou short messages carry AIS data. This paper proposes an AIS message compression algorithm based on Beidou-3. The algorithm centers on the information carried by the AIS message and references the communication capacity of the BeiDou short message, conducting compression processing on message types, message fields, and message transmission frequency according to different message characteristics classification. A Matlab simulation platform was constructed to validate and analyze the compression algorithm. The simulation results show that the information bit quantity of ship dynamic messages was reduced to about 40%–50% after field compression, and static messages were reduced to about 7.5%–10% of the original. Furthermore, the types of messages transmitted after type compression were basically consistent with the message types in the actual collected data. Therefore, after AIS message compression, efficient and reliable transmission of data within AIS signal coverage blind spots can be achieved.