A surface with a smart wettability transition has recently been proposed to enhance the boiling heat transfer in either macro- or microscale systems. This work explores the mechanisms of bubble nucleation on surfaces with wettability transitions at controlled temperatures by molecular simulations. The results of the interaction energy at the interface and potential energy distribution of water molecules show that the nanostructure promotes nucleation over the copper surface and causes lower absolute potential energy to provide fixed nucleation sites for the initial generation of the bubble nucleus and shortens the incipient nucleation time, as compared to the mixed-wettability or hydrophilic nanostructure surface. An investigation on more nanostructured surfaces shows that a surface (F) with a wettability transition temperature of 620.0 K has the shortest average incipient nucleation time at 1672 ps with a wall temperature of 634.3 K. The surface with tunable wettability has also a high interfacial thermal conductance at low superheats, but it may not promote the critical heat flux at high superheats. The heat-transfer performance of the smart surface is better than the plate, the hydrophobic nanostructure, and the mixed-wettability surfaces, while it is lower than the hydrophilic nanostructure surface. This proposes a new method and provides insight for promoting bubble nucleation on a surface with temperature-dependent wettability.