A three-dimensional information processing apparatus includes: a bottom surface intersection point calculation unit calculating intersection points between segments formed by a set of vertices for a terrain model generated by a terrain vertex synthesis unit and outer peripheral segments of a bottom surface of a structure model extracted by a structure bottom surface extraction unit; an all-point height calculation unit calculating heights of the terrain model at the intersection points calculated by the calculation unit and at the vertices constituting the bottom surface of the structure model; a reference height calculation unit calculating a reference height in three-dimensional information on a predetermined area from the heights of the terrain model; and a structure height correction unit correcting the height of the structure model in use of differences between the reference height and the heights of the terrain model.