Abstract: Recent advances in micro/nano-fabrication have positioned porous structures as critical components for boiling heat transfer enhancement. However, experimental studies face challenges in independently evaluating the separate contributions of intrinsic material wettability and pore geometry due to their inherent interdependence. To address this limitation, the molecular dynamics simulations were employed to systematically differentiate and compare the distinct roles of these factors in microscale wicking and boiling dynamics. Two nano-porous configurations, such as nanofoam (pore size: 5-50 Å) and ordered nanomesh (uniform pore size: about 20 Å), were constructed with identical porosity (about 60%) using LAMMPS. Three intrinsic wettability states were implemented by precisely modulating the solid-liquid Lennard-Jones interaction energy (ε): hydrophilic (ε=0.046 eV, contact angle 0°), neutral (ε=0.004 eV, 86.84°), and hydrophobic (ε=0.001 04 eV, 161°). Simulations follow a rigorous three-stage protocol: system equilibration (10 ns at 90 K), wicking dynamics under NVT ensemble, and boiling under NVE ensemble with controlled heating (from 90 K to 300 K). Wicking analysis demonstrates that hydrophilic surfaces significantly amplify capillary forces and liquid retention. The hydrophilic nanomesh structure achieves full saturation in 15 ns, 5.6 times faster than other cases (＞84 ns), which can be attributed to its uniform pores optimally balancing capillary pressure and permeation efficiency. Conversely, the nanofoam structure maintaines partial functionality under neutral wettability due to localized capillary enhancement in sub-20 Å pores, absorbing 12 105 liquid atoms (4.6 times more than the neutral nanomesh’s 2 135 atoms). Hydrophobic structures exhibit negligible wicking (＜400 atoms), sustaining Cassie states. Temperature profiles along the Z-axis reveal that hydrophilic surfaces promote uniform thermal distribution (ΔT＜5 K across 6 nm films), while neutral/hydrophobic cases develop steep gradients (＞20 K/Å near interfaces). Boiling performance analysis establishes the hydrophilic nanofoam as optimal, delivering a peak heat flux exceeding other cases by over 21%. This results from maximized solid-liquid contact area and exceptional liquid retention: over 84% of absorbed liquid remained confined within nano-pores post-evaporation, preventing dryout. Wettability regulates phase change regimes: Hydrophilic cases exhibit sustained evaporation without vapor-layer formation, whereas neutral/hydrophobic cases undergo explosive boiling triggered by localized overheating in thicker liquid films (＞15.5 nm), culminating in vapor-film lift-off and critical heat flux degradation. Pressure variation rates further confirm these mechanisms, with hydrophobic cases showing 3 times lower energy transfer efficiency than hydrophilic counterparts. This study conclusively demonstrates that nanoscale boiling enhancement requires synergistic optimization of intrinsic wettability and pore architecture. Hydrophilic surfaces are essential for strong liquid adhesion, while engineered pore heterogeneity (e.g., foam-like structures) sustains capillary-driven liquid supply under moderate wettability. These insights, clarifying the independent and combined effects of wettability and structure, provide atomic-scale foundations for designing high-flux thermal management devices in nuclear reactors and microelectronics cooling systems.