Molecular dynamics simulation is employed to investigate the heat transfer characteristics of nanofluids in flow boiling. A nanofluids model consisting of both suspended and deposited nanoparticles is established to investigate the mechanisms of nanoparticles in improving the heat transfer of flow boiling. The effects of driving force (i.e. flow velocity) and heating temperature on the heat transfer of flow boiling are analyzed. Results show that both flow velocity and heating temperature have an effect on the heat transfer of flow boiling at lower heating temperature. While with an increase in the heating temperature, the heat flux depends on the higher heating temperature extensively. Furthermore, compared with the base fluid, the heat transfer is enhanced by nanofluids, and the enhancement ratio in flow boiling (F≠0) is higher than that in pool boiling (F=0). A higher frequency of bubble nucleation in nanofluids enhances the thermal convection at the near-surface region. Moreover, the surface wettability is improved by the deposited nanoparticles to increase the efficiency of heat transfer between the surface and the liquid. For suspended nanoparticles, their translational and rotational motions in flow boiling are much stronger than those in pool boiling, which can further enhance the heat transfer of nanofluids.