The invention relates to a spread spectrum encoding GPS signal synchronization system. The spread spectrum encoding GPS signal synchronization system comprises a power source module (1), a GPS antenna system module (2), a GPS receiving system module (3), a stable and constant crystal oscillator module (4), a GPS clock module (5), a GPS information extraction module (6), a pulse counting module (7), a digital display module (8), a time calculating module (9), a data comparing module (10), a digital tube circuit module (11), a synchronization time setting module (12), a key control circuit module (13), a signal transmitting module (14), a signal receiving module (15) and an information storage module (16). According to the spread spectrum encoding GPS signal synchronization system of the invention, time information is extracted through using the GPS, synchronization time is set manually, and therefore, strict working time synchronization of a transmitter system and a receiver system in the spread spectrum encoding system can be realized.