AbstractTo reduce the security authentication time cost, forwarding delay, and enhance message security of Beidou communication short messages, this paper proposes a Beidou communication short message encryption technology based on SM9 (Mobile Code Secure Communication). This technology uses split hierarchical clustering algorithm to cluster the short message data of Beidou Communication, in order to unify the processing of similar short message data and improve the encryption efficiency of subsequent short messages. Based on the data clustering results, this paper constructs a short message forwarding verification model using the SM9 identification password algorithm, and provides the message content of the communication application protocol and the communication receiving information protocol to achieve low‐cost and efficient forwarding verification. In addition, this article improves the initial value selection of Logistic chaotic mapping by coupling the tent map with coupled mapping lattice (CML) in the spatiotemporal chaos model to generate a chaotic initial value sequence, thereby expanding the key space, enhancing the ability to resist exhaustive attacks, enhancing the randomness of the generated key parameters, and optimizing the encryption effect of short messages. The experimental results show that the short message security authentication time of the technology proposed in this article is basically controlled within 25 ms, and the minimum forwarding delay is only 23.9 ms, which can effectively resist attacks and improve the security of Beidou communication.