Digital rock analysis using X-ray computer tomography (CT scan) is an ongoing topic for studying the porous media in geothermal, natural gas, and petroleum industries. This study provides a novel approach to calculating fluid saturation in low permeability cores utilizing X-ray computed tomography. In the present study, synthetic low permeability cores were used to analyze two-phase saturation at atmospheric pressure and temperature. In the experiments, no dopant was used for visualizing different phases. As a novelty of the paper, PHREEQC geochemical software was employed to verify the saturation of X-ray CT scanning through modeling the geochemical reaction between aqueous and gaseous phases. This study presents a novel and reliable approach to verify the saturation of X-ray CT scan through geochemical modeling. The results of this study also prove that using the saturation of mass balance as the initial condition of the geochemical modeling leads to an excellent agreement between the saturation of CT scan and geochemical modeling. According to the results obtained, there is a 24% difference between gas saturation in CT scan and mass balance method, while such discrepancy is only 13% between gas saturation in CT scan and geochemical modeling.