A three-dimensional shape data processing apparatus includes a data input unit configured to input data of a first tomographic image group including a plurality of tomographic images and data of a second tomographic image group including a plurality of tomographic images, wherein at least a part of an image capturing area of the second tomographic image group is overlapped with at least a part of an image taking area of the first tomographic image groups, and a combination unit configured to combine first three-dimensional shape data and second three-dimensional shape data into one piece of three-dimensional shape data according to an estimated accuracy estimated values of the first and second three-dimensional shape data at a plurality of positions.