Phobos, one of the Martian moonlets, has been the focus of long-standing scientific investigation, particularly regarding its origin: whether it was formed by a giant impact or a captured asteroid. In this study, we investigate the long-term internal evolution of Phobos over 4.3 billion years using a 3-dimensional thermal diffusion and water transport model, named ASTRA. The model newly implements reflected visible light and infrared radiation from Mars, orbital evolution of Phobos, water vapor adsorption on rock grain surfaces, and suppressed permeability due to the surface dust layer in addition to the previous study, allowing us to simulate different grain sizes of 1, 10, 100, and 1000 μm, adsorption coefficients of 1 and 10 kg m−3, and initial water contents of 0.1, 1 or 10 wt%.Our simulation results revealed that without the water vapor adsorption effect, the water inside Phobos would be lost over several billion years for an initial water content of 0.1 wt%. However, when water vapor adsorption was considered, scenarios emerge in which Phobos could retain water to the present day. In the case of a grain size of around 100 μm, Phobos could still continuously release water flux of 10−4–10−3 g s−1 for an initial water content of 0.1 wt%, and 10−2–1 g s−1 for an initial water content of >1 wt%. Furthermore, our research shows the possibility of subsurface condensed water ice in deep high latitude regions and the formation of a gas torus by escaping water-related molecules. If the future MMX mission can measure the water-related ions near the gas torus of Phobos with much >104 cm−2 s−1, the origin of Phobos is most likely the captured asteroid with an initial water content of >1%. For further detailed analysis, our results emphasize the importance of exploring surface soil parameters through soil sample return by the MMX mission.