We propose a new image registration method based on joint respective window sampling (RWS) and modified motion compensation (MMC) in an interferometric inverse synthetic aperture radar (InISAR) imaging system using two antennas. The causation and quantitative analysis of the offset between two ISAR images of different antennas along the baseline are analyzed. In the proposed method, the RWS method, according to the measured distance between the target and different antennas, compensates the offset in the range direction. The MMC method is adopted to eliminate the offset in the Doppler direction. Simulation results demonstrate that the offset between the two ISAR images can be compensated effectively, consequently achieving a high-quality three-dimensional InISAR image.