A 3D modeling apparatus includes: a generator configured to generate 3D models of a subject based on pairs of images; a selector configured to select a first 3D model and a second 3D model from the 3D models, wherein the second 3D model is to be superimposed on the first 3D model; an extracting unit configured to extract first feature points from the first 3D model and extract second feature points from the second 3D model; an acquiring unit configured to acquire coordinate transformation parameters based on the first and second feature points; a transformation unit configured to transform coordinates of the second 3D model into coordinates in a coordinate system of the first 3D model, based on the coordinate transformation parameters; and a combining unit configured to superimpose the second 3D model having the transformed coordinates on the first 3D model.