A network based motion control system, in which the NC interpolation node and the servo control nodes were connected by IEEE 1394, was analyzed and tested, and it is found there exists problem in multi-node synchronization. In order to solve the problem, this paper proposed a protocol for the field-bus and a synchronization mechanism based on CNC-RTX clock timing. Real-time communication among CNC nodes and four sub-nodes was realized, and synchronization errors among CNC nodes and sub-nodes caused by clock floating, network induced delay, and different timing mechanism were avoided as well. Experimental results show that the application layer protocol and the synchronization mechanism can realize high performance in communication with less synchronization errors.