<p>Baked sweet potato is a commonly consumed product worldwide. However, an optimal method for storing raw sweet potatoes is still under research. Previously investigated method of freezing for sweet potatoes before baking revealed that the physical properties of baked sweet potatoes were modified. However, the investigation was conducted only on one cultivar under one baking condition, and the dependence of the processing characteristics on cultivar differences and other baking conditions remains unknown. In order to clarify the processing characteristics, their physical properties, moisture contents, mechanical property, tissue macrostructures based on three-dimensional (3D) X-ray computed tomography (CT), were investigated after pre-frozen-baking (PFB) treatment at 150 and 200°С for several baking periods using two cultivars (“Beniazuma” and “Beniharuka” (BH)). The moisture content of the cultivars mainly depended on the baking conditions. Although the maximum stress decreased in the early stage of baking, it was greatly increased in latter stage of baking. The moisture content and the maximum stress followed a quadratic relationship (<i>R</i>² = 0.75–0.99). The vertex coordinate of the corresponding quadratic equation might indicate an optimal condition for obtaining a soft product while retaining moisture, especially for the “BH”. The 3D X-ray CT analysis revealed that the pre-freezing treatment could inhibit the large porosity part of the samples after baking. This study could demonstrate the potential of PFB treatment to produce a new food material using sweet potatoes with unique texture and structure.</p>