The thermal design of reactor fuel assembly relies on accurate heat and mass transfer models. However, current numerical simulation commonly utilize simplified boundary conditions to solve for the fluid domain, neglecting the impact of non-uniform heat transfer characteristics caused by fluid–solid conjugate heat transfer. Therefore, this study establishes a fluid–solid conjugate heat transfer and two-phase flow Euler-Euler model based on STAR-CCM + to realize coupled calculations of fuel heat conduction and subcooled flow boiling. This numerical approach was validated by a typical fuel rod simulation. Then a 3-D model of rod subchannel was built and the detailed three-dimensional thermal–hydraulic characteristics and the distribution of wall heat flux and its allocation mechanism between the gas and liquid phases under different axial power distribution were investigated. The results indicated that the heat transfer characteristics on the circumferential position of the rod surface are angle-dependent and exhibit a periodic distribution. The wall heat flux fluctuates around an average value as the angle changes, and is mainly dominated by evaporation heat transfer and quenching heat transfer. Additionally, under high subcooling situation, the fluid domain of the non-heated section will transfer heat from the high temperature region in the circumferential direction to the low temperature region through the solid domain. The simulation method established in this paper can provide a new auxiliary tool for optimizing the thermal design of fuel assembly or subcooled flow boiling heat transfer systems.