Provided is a surgery assistance system to perform relatively fast and accurate alignment between three-dimensional surface shape data acquired by measurement using a three-dimensional surface shape scanner and three-dimensional internal shape data acquired in advance, even when the position of the patient and the surface shape of the skin of the patient change during the surgery. A surgery assistance system (1) includes a three-dimensional surface shape scanner (20) for acquiring three-dimensional surface shape data by measuring a three-dimensional surface shape of a patient (60) and a computing device (40) for processing the data from the three-dimensional surface shape scanner. The computing device stores therein three-dimensional internal shape data of the patient that is acquired in advance by measurement using a three-dimensional tomography scanner (30). The computing device has a unit that aligns the three-dimensional internal shape data and the three-dimensional surface shape data with each other by using data of a portion where a distance between a skeleton and a skin surface is small in the three-dimensional internal shape data and three-dimensional surface shape data corresponding to this portion.