Abstract: First of all, the working principle of the single pulse tracking system,in which TM01 mode is the common mode and TE21 mode is the differential mode, was demonstrated in the paper. Secondly, a designing scheme of the digital tracking receiver was presented. The influence on the tracking performance by phase difference between the common channel and the differential channel was analyzed. And a zero cross point detection plus digital phase shift compensation method was proposed, which could be implemented in a tracking receiver design. The performance of this method was carried out. In experimental prototype, the cross coupling comparison before the phase compensation and after was presented at last. This method which is given in the paper has very good stability and is independent of frequency of the tracking system. The application in experimental system shows that this method can calibrate phase error with a very high speed. And the cross coupling performance of the system satisfies the design requirement. The tracking process is stable and reliable.