We demonstrate a calibration method for endoscopic three-dimensional shape measurement with cone beam projection. In this method, changes in the shape of the optical sectioning profiles are quantified and fitted while scanning a calibration board in the depth direction, using a cubic function. In accuracy tests using a flat plate and a ring reference gauge, the proposed method obtains an accuracy of 0.02 mm in the depth dimension and 0.09 mm in the radial dimension. These results represent 88% and 55% improvements compared to previous analysis. For medical applications, an ear examination simulator was employed, and our measurement results were compared to ground truth data obtained by microfocus X-ray computed tomography. The surface deviation of our method relative to the ground truth data was ±0.36mm during manual operation. A comparison of the measurement results before and after calibration revealed an improvement in the peak agreement with the ground truth data, with the deviation shifting from 0.2 mm to −0.05mm. Our strategy achieves a digital transformation of 3D endoscopy, which would benefit a number of medical fields.