In this work, the color difference phase separation (CDPS) approach is proposed to segment the solid and pore phases. Pore‐scale variables are defined to describe the microstructural characteristics. Novel relations to quickly determine the deformation moduli and thermal conductivity are established. Digital–virtual modeling to investigate the mechanical and thermal properties is addressed. The correlation between pore‐scale variables and the mechanical and thermal properties is investigated. Results show that the calculated shear and Young's moduli decrease and the computed Poisson's ratio increases as porosity increases. The deformation moduli and thermal conductivity increase with increasing pore radius for different types of rocks. Excellent consistencies are found between the digital–virtual and realistic experimental results. The proposed method provides useful tools to fast and accurately determine the deformation moduli and thermal conductivity, which is helpful for the underground space and deep energy resource explorations.