The invention relates to an anti-interference method of a synchronous clock device of an intelligent substation. Two layers of active defensive measures are taken to resist the network interference. The anti-interference method comprises the following steps that firstly, the number of messages with the same CRC is counted, whether the number is larger than a threshold value or not is judged, and if yes, the messages are shielded in the set time; secondly, messages with the same target MAC address are detected, the flow of the messages is counted, whether the flow of the messages is larger than the threshold value or not is judged, and if yes, the messages are shielded in the set time; shaking removing and overtime process are carried out on an input pulse per second to resist the electromagnetic interference, and the stability of time tick signals is kept. By means of the method, under the situation of electromagnetic interference and network flow interference, time tick precision of the synchronous clock device is kept, and the synchronous clock device can stably and reliably run.