1. An image alignment device comprising: a storage unit for storing a 3D deformation model of a target organ representing nonlinear 3D deformation of the target organ due to respiration, and which has been generated based on information about movement of the target organ due to respiration of a plurality of patients; an image acquisition unit for acquiring a first 3D image and a second 3D image obtained by imaging a target organ of a patient in different phases of respiration; a position estimation unit for estimating the positions of the pixels on the second 3D image representing the same positions on the target organ as a plurality of sampled pixels in a target organ region on the first 3D image using displacement due to changes in phase of points on the 3D deformation model corresponding to the positions on the target organ represented by the pixels; and an alignment unit for performing non-rigid alignment between the first 3D image and the second 3D image using the estimated positions of the pixels on the second 3D image.