Distributed array radar provides new prospects for three-dimensional (3D) inverse synthetic aperture radar (ISAR) imaging. The accuracy of image registration, as an essential part of 3D ISAR imaging, affects the performance of 3D reconstruction. In this paper, the imaging process of distributed array ISAR is proposed according to the imaging model. The ISAR images of distributed array radar at different APCs have different distribution of scatters. When the local distribution of scatters for the same target are quite different, the performance of the existing ISAR image registration methods may not be optimal. Therefore, an image registration method is proposed by integrating the feature-based method and the area-based method. The proposed method consists of two stages: coarse registration and fine registration. In the first stage, a dominant scatters model is established based on scale-invariant feature transform (SIFT). In the second stage, sub-pixel precision registration is achieved using the local correlation matching method. The effectiveness of the proposed method is verified by comparison with other image registration methods. The 3D reconstruction of the registered experimental data is carried out to assess the practicability of the proposed method.