Interrupted Sampling Repeater Jamming (ISRJ) is an electronic countermeasure against radar echo signals that generates many false targets to mask the real target echoes, which seriously affects radar target detection performance. Most of the ISRJ suppression methods require accurate estimation of the signal parameters, and the estimation methods are complex. Based on the characteristics of discontinuous ISRJ sampling and orthogonality between multi-carrier phase coding (MCPC) signal's subcarriers, we propose a method for ISRJ identification and suppression based on an improved MCPC signal. By analyzing the pulse compression of the echo, we found that different types of intermittent sampling interference have different peaks after pulse compression. Based on this feature, we introduce Fractional Fourier Transform to filter out interference. Theoretical analysis and simulation results show that the method can effectively suppress the three classical ISRJ interferences. The method suppresses ISRJ during echo processing without any parameter estimation for real scenes and has stronger robustness than other existing schemes.