By using the 1 Pulse Per Second(1PPS) received from Global Positioning System(GPS), the disciplining method is studied for common secondary frequency source Temperature Compensated Crystal Oscillator(TCXO) and Coherent Population Trapping(CPT) atomic clock. A disciplining scheme of phase-locked loop is designed. The time difference between 1PPS from local frequency division and that received by GPS receiver is measured by Time-Digital Converter(TDC) to realize the locking of local signal to GPS time signal. TCXO has achieved frequency stability of 8.5 ′ 10-12 at 10 ks, and the average frequency accuracy at 35 ks after disciplining has been improved by more than 4 times. In addition, the noise model of CPT atomic clock is deeply studied and simulated through Matlab. The corresponding relationship between white frequency noise and random walk frequency noise on Allan variance curve is established. The results after disciplining by average filtering and Kalman filtering on CPT atomic clock are compared, and the frequency stability increases by an order of magnitude at 50 ks.