The Controller Area Network （CAN） based Autonomous Underwater Vehicle （AUV） dual-machine redundant control system requires a certain degree of clock synchronization， and it lacks an Ethernet interface that implements IEEE 1588 （precision clock synchronization protocol standard for network measurement and control systems）. In view of this problem， a precision clock synchronization method based on CAN and IEEE 1588 principle was proposed. Firstly， the core code of CAN-based clock synchronization software was written on the basis of the principle of IEEE 1588. Then， the key data of interaction were encoded and compressed to 8 bytes based on the data length of CAN standard frame. Finally， the synchronization performance of the CAN-based dual-machine clock synchronization software was tested and compared with that of the Ethernet-based dual-machine clock synchronization software. Test results on actual hardware platforms show that by using the proposed method， the clock synchronization accuracy of dual-machine redundant control system can reach and maintain within 25 μs， satisfying the 1 ms synchronization accuracy requirement of dual-machine redundant control system. It can be seen that the proposed method can guarantee the clock synchronization accuracy of dual-machine redundant control system.