In the field of heat dissipation of electronic devices with high heat flux, passive microchannel heat dissipation technology has the advantages of high stability and low energy consumption, in which phase change process brings high heat transfer efficiency. To explore the mechanism of phase change heat transfer in capillary nanochannels, the bubble dynamic behavior and influence factors under capillary flow in nanochannels are studied using molecular dynamics method. It is found that higher heating temperatures will accelerate the nucleation and growth of bubbles. At the same heating temperature, with the enhancement of wettability, the liquid changes from pure flow phenomenon to nuclear boiling, and even “drying” phenomenon. The enhancement of wettability is beneficial to the nucleation and growth of bubbles, and improves the heat transfer performance. But it has a nonlinear effect on the liquid flow which first promotes and then inhibits. In addition, it is found that the generation of bubbles will greatly enhance the heat transfer efficiency. This study is of great significance for improving the passive phase change heat transfer mechanism under capillary flow in nanochannels.