With the improvement of the accuracy of atomic frequency standard and satellite navigation, the high-resolution phase comparison method is necessary. Using the phase synchronous detection principle, a super-high resolution phase comparison method between frequency standards is proposed based on the greatest common factor frequency, phase group processing and a common frequency source and so on. This method is mainly dependent on the stability of the common frequency standard and its frequency. The ±1 count error can be eliminated effectively. Therefore, higher than 1 ps resolution can be easily reached with a simple instrument. Experimental results show higher than 10⁻¹⁵/h precision can be obtained in the long-term frequency standard comparison and the measuring precision can reach 10⁻¹⁷ for several days of comparison.