In wireless sensor networks in industrial control systems, wireless communication security is challenged due to the broadcast nature of the wireless channel, where information is more easily eavesdropped by illegal nodes on the network. The article establishes a secure communication system based on ZigBee wireless communication technology applied to wireless sensor networks in industrial control systems. In order to improve the secure communication performance of wireless sensor networks, this paper combines the Merkle tree with the μTesla protocol to establish a key management scheme for wireless communication. Then from the node trust degree, the node two-way authentication mechanism for data transmission is constructed by combining the digital signature algorithm. For the effectiveness of the secure communication mechanism of wireless sensor networks, this paper carries out data analysis through performance testing. The key management scheme takes about 17.37 μs and 3.24 μs to add and revoke a key, respectively, and the local optimal value of user time consumption is 7.26 s when the connectivity frequency is 12 min and the revocation threshold is 60. The average value of the node bidirectional authentication mechanism can reach 96.17% for the accuracy of identifying the malicious nodes in the wireless sensor network, and the bit error rate is lower than 0.5 % for the communication transmission with the mesh topology. The bit error rate is less than 0.1%. The introduction of Merkle tree and digital signature algorithms into the construction of secure communication mechanisms in wireless sensor networks can significantly improve the data transmission security performance of industrial control systems.