The invention belongs to the technical field of intelligent substation network security, and particularly relates to a transformer substation adaptive network based on difference detection and a secure clock synchronization method thereof. The network comprises optical network units ONU, a synchronous optical line terminal OLT and an EPON protocol processor; two interfaces of each ONU have the same state all the time, and redundancy configuration of master and slave links is adopted; and the EPON protocol processor communicates with the ONU through a multipoint control protocol. The method comprises the following steps: the EPON protocol processor transfers a timestamp to each ONU; the OLT compares whether two interfaces of the ONU receive messages within a specified time difference and whether the synchronous timestamps carried in the messages are consistent, if not, a security threat exists, and the time check is not adjusted; and if so, the OLT detects whether a round trip time RTT difference exceeds a specified threshold, if so, the security threat exists, and the time check is not adjusted; and if the RTT difference does not exceed the threshold, ONU registration is completed, and normal communication is started.