As a key object on the ocean, regulating civilian and military ship targets more effectively is a very important part of maintaining maritime security. One of the ways to obtain high-resolution images of ship targets is the inverse synthetic aperture radar (ISAR) imaging technique. However, in the actual ISAR imaging process, ship targets in a formation often lead to complicated motion conditions. Due to the close distance between the ship targets, the rough imaging results of the targets cannot be completely separated in the image domain, and the small differences in motion parameters lead to overlapping phenomena in the Doppler history. Therefore, for situations in which ship formation targets with little difference in motion parameters are included in the same radar beam, this paper proposes a multi-domain joint ISAR separation imaging method for multi-ship targets. First, the method performs echo separation using the Hough transform (HT) with the minimum entropy autofocus method in the image domain. Secondly, the time–frequency curve is extracted in the time–frequency domain using the short-time Fourier transform (STFT) for time–frequency analysis, which solves the problem of the ship formation targets being aliased on both echo and Doppler history after range compression and achieves the purpose of separating the echo signals of the sub-ship targets with high accuracy. Eventually, better-focused images of each target are obtained via further motion compensation and precise imaging. Finally, the effectiveness of the proposed method is verified using a simulation and measured data.