To study the processes of boiling on a smooth surface with contrast wettability, a hybrid model was developed based on Lattice Boltzmann method and heat transfer equation. The model makes it possible to describe the phenomena of natural convection, nucleate boiling, and transition to film boiling, and, thus, to study heat transfer and the development of crisis phenomena in a wide range of surface superheats and surface wetting characteristics. To find the optimal configuration of the biphilic surface, at the first stage a numerical simulation was carried out for a single lyophobic zone on a lyophilic surface. The dependences of the bubble departure frequency and the departure diameter of the bubble on the width of the lyophobic zone were obtained, and its optimal size was determined. At the next stage, the boiling process on an extended surface was studied in the presence of several lyophobic zones of a given size with different distances between them. It is shown that in the region of moderate surface superheat, the intensity of heat transfer on biphilic surfaces can be several times (more than 4) higher compared to surfaces with homogeneous wettability. Based on numerical calculations, an optimal configuration of the biphilic surface with the ratios of the lyophobic zones’ width of the order of 0.16 and the distance between the lyophobic zones in the range of 0.9–1.3 to the bubble departure diameter was found.