The increasing heat flux of electronic devices poses significant challenges in thermal management. Passive heat dissipation technology based on capillary drive has been widely concerned because it does not require external driving force and stability. However, due to the small size of the internal capillary structure, typically in the micro and nano scales, and the significant scale effect, further research is needed to understand the mechanism of internal boiling heat transfer. This study systematically investigates the boiling process of liquid in nanochannels under capillary flow with varying wettability using molecular dynamics simulations. It is found that increasing the energy coefficient (c) causes a greater accumulation of atoms near the wall, thereby enhancing the efficiency of solid–liquid heat transfer. The bubble has a larger stable volume as c increases and will burst in the case of high c. As c increases, the region of high potential and kinetic energy expands more rapidly, reducing the time it takes for bubble nucleation and rupture. The behavior of bubbles is significantly influenced by capillary flow, which is also influenced by wettability. When c = 0.9, the flow velocity reaches its maximum before bubble nucleation occurs. It leads to a more homogeneous heat transfer, resulting in a higher location of bubble nucleation. Furthermore, the presence of capillary forces increases the average potential energy of surrounding liquid atoms, thereby enhancing the growth rate of the bubble. This study provides a theoretical basis for the optimal design of capillary-driven two-phase heat dissipation devices.