Distributions of thermo-physical properties: such as porosity and thermal conductivity of Japanese apricot and pear during storage were determined based on X-ray CT image analysis. Japanese apricot was stored at 25 °C, whereas pear was stored at 25 °C and 5 °C. Average CT value was determined based on a series of X-ray CT images captured for each whole fruit. At the end of storage period, the average CT value decreased in Japanese apricot and pear at 25 °C, whereas it was the almost same as pear stored at 5 °C. Porosity increased, whereas thermal conductivity slightly decreased at 25 °C in Japanese apricot and pear. As a result of the experiment, it seemed that the internal structure of pear stored at 5 °C was well maintained during storage. Conversely, void space progressed in Japanese apricot and pear during storage at 25 °C. The porosity and thermal conductivity distributions were visualized based on the CT image during storage.