An ellipsoidal mirror is a soft X-ray reflective focusing device. We are developing precise ellipsoidal mirrors based on an electroforming process. To improve the fabrication process, three-dimensional shape measurements with a high accuracy are required. In this research we develop a method to measure ellipsoidal shapes by industrial X-ray computed tomography (CT). The X-ray CT process consists of measuring the mirror shape and determining the parameters of the ellipsoid. We also evaluate the reproducibility of X-ray CT measurements and clarify that the accuracy is at the 5-m level.