The invention relates to an automatic checking method for clock synchronization, comprising the following steps: (1) regularly acquiring clock signals sent by a Beidou signal source, a GPS signal source and an SNTP signal source; (2) performing subtraction to the clock signals of the Beidou signal source and the GPS signal source and evaluating the absolute value of the difference; at the same time, performing subtraction to the clock signals of the Beidou signal source and the SNTP signal source and then evaluating the absolute value of the difference and finally judging the results of the two differences; and (3) constantly repeating steps (1) and (2). The operations in the present invention can efficiently avoid the problems in the existing technology, guarantee the consistency and accuracy of system time, and guarantee the stable and safe operation of the system and the normal operation of other power grid businesses.