The invention discloses a high-precision time synchronization system and method in an embedded system. The synchronization system is formed by cooperation of a high-precision time source, an auxiliary counter, and a time synchronization and maintenance module. During time synchronization, firstly, the time of the high-precision time source and the time of the auxiliary counter at the same time are obtained; then the time drift and the time offset of the auxiliary counter are calculated and maintained; and the time of the auxiliary counter is obtained according to the requirement, and the high-precision system time is obtained according to conversion of the time drift and the time offset. Therefore, a high-precision time synchronization scheme is formed, high-precision time maintenance is realized through real-time calculation and correction of clock errors, the stability is high, the cost is low, and problems of poor precision of a clock chip, and easy influence of temperature and aging on the precision are effectively solved.