Abstract: In view of problems of poor long-term stability of OCXO and susceptibility to interference and poor short-term stability of GPS, synchronous clock system of transient electromagnetic based on GPS and OCXO was designed. "ARM+CPLD" mode is used as core processing unit, and frequency deviation measurement module is used to detect crystal frequency of high frequency signal between two adjacent second pulses, taking GPS second pulse signal as benchmark. The self-adaptive PID controller is used to adjust output frequency of crystal oscillator, which effectively solves the problem that accuracy of control voltage of OCXO is affected because single frequency deviation is too large, and improves stability of the system. Second pulse signal is used as a timer to reset divider at regular intervals, which achieves automatic elimination of cumulative error of OCXO and ensures phase synchronization of output signal. The test results show that the system achieves high precision synchronization of transient electromagnetic transmitter and receiver, synchronization precision is about 270 ns when GPS signal is normal, and synchronization precision is about 350 ns when GPS signal is lost. The system has been successfully applied to transient electromagnetic detection system, a large number of practical application results show that the system has good stability and high synchronization accuracy.