In this study, phase change characteristics of thin liquid argon film over nano-porous substrates has been investigated through Molecular Dynamics Simulation (MDS). Nano-porous substrate having hexagonal shaped nano-pores with variable pore size, height, number, and surface wettability has been considered. Geometric variation of the nano-porous substrate is characterized in terms of two parameters such as the void ratio and the height to arm thickness. The wettability variation is represented by the wall-fluid interaction strength relative to that of fluid-fluid interaction namely, hydrophilic, hydrophobic and superhydrophobic. Present study reveals that the occurrence of explosive boiling has been found to depend both on the surface topology as well as surface wetting condition. For hydrophilic and hydrophobic nano-porous substrates, explosive boiling phenomena have been observed while for superhydrophobic cases diffusive evaporation has been noted. Phase change characteristics have been analyzed in terms of transient atomic distribution and Mean Squared Displacement (MSD), system temperature, wall heat flux, evaporation rate and onset of explosive boiling designating the separation of liquid film from the wall. The phase change mode for hydrophilic and hydrophobic nano-porous substrates changes from sustained explosive boiling to pseudo explosive boiling with the decrease of void ratio and increase in height. Furthermore, it has been observed that nano-porous substrates with lower void ratio offer improved thermal performance, as designated by higher wall heat fluxes along with other transport parameters. In this regard, increasing the height of the nano-porous substrate has been found to have even much stronger effect. Finally, the underlying mechanisms behind better thermal performance of nano-porous substrates have been studied by analyzing early-stage bubble nucleation and evolution inside of the nanopores.