How surface wettability affects boiling heat transfer of thin liquid film on a nanoscale remains a challenging research topic. In this work, the effects of wettability on the nanoscale boiling heat transfer for a thin liquid film on hydrophilic surface and hydrophobic surface are investigated by molecular dynamics simulation. Results demonstrate that the hydrophilic surface has better heat transfer performance than the hydrophobic surface. It has a shorter boiling onset time, higher temperature, heat flux, interfacial thermal conductance, and weakened interfacial thermal resistance. The hydrophilic surface throughout has higher critical heat flux than the hydrophobic surface in both macro-system and nanoscale system. Besides, a two-dimensional surface potential energy is proposed to reveal the mechanism of wettability affecting the boiling heat transfer. The absolute value of potential energy in one regular unit of hydrophilicity (–0.34 eV) is much higher than that of hydrophobicity (–0.09 eV). That is the crucial reason why the heat transfer enhancement via improving surface wettability should be primarily the powerful surface potential energy. In addition, the interaction energy is calculated to further address the nucleation mechanism and heat transfer performance for liquid film on different wettability surfaces. The interaction energy values are ordered as I_phi (1.57 eV/nm²) > I_water (0.48 eV/nm²) > I_pho (0.26 eV/nm²), indicating that the better heat transfer performance of hydrophilic surface is because of the large interaction energy at the solid/liquid interface. Besides, the bubble nucleation on a hydrophilic surface needs absorbing more energy and occurs inside the thin liquid film, while it needs absorbing less energy and triggering off at the solid/liquid interface with hydrophobicity. Those uncover the principal mechanisms of how wettability influences the bubble nucleation and boiling heat transfer performance on a nanoscale.