The invention provides a method and system for shortening a serial compensation gap trigger integral time delay. Currents of sampling points in a serial compensation apparatus are sampled through an electronic current transformer, a sampling digital quantity is output, and then, the sampling digital quantity is forwarded to a serial compensation protection apparatus through a merging unit; the serial compensation protection apparatus decodes and determines the sampling digital quantity, and according to a determination result, generating a gap trigger command; a gap trigger apparatus decodes the gap trigger command, generates high-voltage pulse signals and controls a sealing gap to be conducted through a pulse transformer, and thus the serial compensation apparatus is protected; and the electronic current transformer, the merging unit, the serial compensation protection apparatus and the gap trigger apparatus are successively connected in series through fibers for direct transmission of the digital quantity, a time delay generated when the digital quantity is converted into an analog quantity and then is sent in the prior art is unnecessary, the overall time delay of serial compensation protective motion can be reduced, and the safety of a capacitor group in the serial compensation apparatus is guaranteed.