To reveal the synergistic roles of nanostructure morphology and mixed wettability in regulating nucleate boiling heat transfer in liquid films, molecular dynamics simulations were performed for six nanostructured composite surfaces. The results show as follows. For fully hydrophobic nanostructures, bubble nucleation is preferentially initiated within the hydrophilic regions of the heated substrate. With respect to geometric effects, the shortest nucleation onset time is obtained for the inverted trapezoidal structure, whereas the longest onset delay is observed for the trapezoidal geometry. This trend is attributed to morphology-induced variations in the effective solid-liquid heat-transfer area and lateral heat dissipation within the liquid film. Moreover, when partial hydrophobicity is incorporated into the nanostructures, the nucleation onset time is markedly shortened, and the most pronounced enhancement in heat transfer performance is achieved by the trapezoidal and inverted trapezoidal configurations. These findings provide fundamental insights for the rational design and optimization of functional surfaces to enhance nucleate boiling efficiency.