Characteristics of water film thickness and stability within nanopores are topics of great interest for evaluation of initial fluid storage in unconventional reservoirs. Although related researches with thin film on flat substrates have been carefully and extensively considered, the thickness and stability of liquid films affected by nanoscale confinement in nanostructured materials, such as clay minerals and tight rocks, have raised lots of questions. In this work, an approach by considering fluid/pore-wall interactions (surface forces) was developed to describe the phase behavior of thin water film transition into liquid condensation. The calculated results reveal that the instability mechanisms of adsorbed films differs inside slits and capillaries. In slit pores, the coalescence of flat wetting films forms under the action of attractive forces by opposite slit surfaces. Whereas in capillaries, collapse of curved wetting films occurs due to the integrative action of surface force and cylindrical capillary force. Due to the additional capillary action, the total surface interactions inside capillaries are higher than that inside silts, which leads to an easier condensation and thicker film thickness in capillaries. Meanwhile, the phase behavior of adsorbed water film within nanoporous montmorillonite and shale were investigated by water vapor (H2O) adsorption isotherms. Specially, the water distribution characteristics inside single nanopore rather than the whole porous media were also investigated based on the difference of pore size distribution (PSD) between dry and moist samples, and these PSD information was obtained by low temperature (77 K) nitrogen (N2) sorption analysis. Our experimental results directly demonstrated the evidence of water condensation in hydrophilic clay samples, e.g., pores < 6–7 nm would be totally blocked by capillary water. However, a “partial condensation” phenomenon was found in shale samples, e.g., the shale nanopores could not been entirely filled by water even under a high-moisture condition (RH = 0.98), which was mainly caused by hydrophobic repulsion of organic minerals. This surface repulsion could prevent water from condensing and likely result in a monolayer water film adsorbed inside these hydrophobic organic nanopores, e.g. graphite. Therefore, in an actual shale system with initial moisture, the storage of water inside organic pores can be neglected while these inorganic micropores blocked by condensate may be unavailable for gas storage or transport.