The invention discloses a brand new orthogonality-training-based clock estimation method of bi-direction relay channel physical layer network coding. In a bi-direction relay channel PNC, two signals arrive at a relay node at different time, and then relative time migration exists. According to the method, firstly, the relative time migration is converted into the difference of two absolute time migrations, secondly, the two absolute time migrations are estimated, and finally, the estimation value of the relative time migration is obtained. According to the estimation of the two absolute time migrations, two estimation algorithms including the optimization sampling point algorithm and the interpolation algorithm based on discrete Fourier transform are put forward. The estimation on any absolute time migration can be achieved through any algorithm. By means of a Matlab simulation platform, the feasibility of the brand new orthogonality-training-based clock estimation method is verified, and the optimal algorithm combination is found. By means of the combination, when the signal to noise ratio is small, the mean square error of the system is very close to the theory lower bound, and meanwhile the calculation amount is small.