Interrupted sampling repeater jamming (ISRJ) is characterized by its coherent processing gains and flexible modulation techniques. ISRJ generates spurious targets along the range, which presents significant challenges to the radar systems. However, existing ISRJ countermeasure methods struggle to eliminate ISRJ signals without compromising the integrity of the real target signal, especially under low-signal-to-noise-ratio (SNR) conditions, resulting in a deteriorated sidelobe and diminished detection performance. We propose a complex-valued encoder–decoder network (CVEDNet) to address these challenges based on signal decomposition. This network offers an end-to-end ISRJ suppression approach, working on complex-valued time-domain signals without the need for additional preprocessing. The encoding and decoding structure suppresses noise components and obtains more compact echo feature representations through layer-by-layer compression and reconstruction. A stacked dual-branch structure and multi-scale dilated convolutions are adopted to further separate the echo signal and ISRJ based on high-dimensional features. A multi-domain combined loss function integrates the waveform and range-pulse-compression information to ensure the amplitude and phase integrity of the reconstructed echo waveform during the training process. The effectiveness of the proposed method was validated in terms of its jamming suppression capability, echo fidelity, and detection performance indicators under low-SNR conditions compared to conventional methods.