A shape data generation method includes: generating a target shape of transformation from plural tomographic images of an object; specifying, from among plural vertices of a first shape that is a reference shape of the object, plural first vertices, each first vertex of which satisfies a condition that a normal line of the first vertex passes through a point that is located on the target shape and is located on a boundary of the object in any one of the plural tomographic images; identifying, for each of the plural first vertices, a second vertex that internally divides a segment between the first vertex and the point; transforming the first shape so as to put each of the plural first vertices on a corresponding second vertex; setting a shape after the transforming to the first shape; and executing the first specifying and the subsequent processings a predetermined number of times.