Volume registration is an essential technology for comparing medical volume data acquired in different days and for combining different types of volume data from various imaging devices. For accurate comparison, it is necessary to correct non-rigid deformation between volume data, since the complex deformation between medical volume data is observed even if they are taken from the same regions of the subject. This paper proposes a novel non-rigid registration method using 3D Phase-Only Correlation (POC). The proposed method achieves accurate and fast volume registration by employing POC-based block matching (with small volume blocks), which can find the voxel correspondence with sub-voxel accuracy between two volume data. The proposed method exhibits higher accuracy and shorter computation time compared with the conventional method, and is effective even for multimodality cases such as CT-MRI registration.