Three-Dimensional (3-D) Interferometric Inverse Synthetic Aperture Radar (InISAR) imaging system based on the orthogonal double baseline can achieve the 3-D geometric reconstruction of a target effectively, which is extremely helpful in target classification and identification. However, only sparse aperture measurements are available in the actual imaging process, which might pose some challenges to the traditional InISAR imaging algorithms. In this study, a new method of 3-D InISAR imaging of a ship with sparse aperture is presented. Minimum entropy algorithms are adopted to realize motion compensation and image coregistration of the sparse echoes. A gradient-based technique is used to achieve highly accurate signal reconstruction for the sparse aperture. A two-Dimensional (2-D) ISAR image was achieved with azimuth compression via the parameters-estimation method, and the 3-D reconstruction of a ship was achieved via the interference approach. The obtained simulation results validate the feasibility of the presented approach.