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Interrupted-sampling repeater jamming (ISRJ) is a kind of intra-pulse coherent deception jamming that can generate false target peaks in the range profile and interfere with the detection and tracking of real targets. In this paper, an anti-ISRJ method based on the intra-pulse orthogonal waveform is proposed, which can recognize common interference signals by comparing sub-signal matched filtering results. For some special scenes where real targets cannot be directly differentiated from false targets, a new recognition method based on the energy discontinuity of the interference signal in the time domain is proposed in this paper. The method proposed in this paper can recognize real and false targets in all ISRJ modes without any prior information, such as jammer parameters, with a small amount of calculation, which is suitable for actual radar systems. Simulation experiments using different interference parameters show that although this method has a 3 dB loss of pulse compression gain, it can completely suppress different kinds of ISRJ interference when the SNR before pulse compression is higher than −20 dB, with 100% target detection probability.