An accurate prediction of core bypass flow is of great importance in the design of very high temperature reactor (VHTR) cores in terms of the fuel thermal margin and safety. In the present study, a unit-cell experiment and computational fluid dynamics (CFD) analysis were carried out to evaluate the amount and distribution of core bypass flow. This study examined the effects of the inlet mass flow rate, block combinations, and thickness of the bypass gap. The prediction capability of the CFD code FLUENT was validated by the unit-cell experimental result. The analysis was extended to the entire core region. In this simulation, a quarter core was simulated using the nonconformal grid method to reduce the computational cost and time. The accuracy and applicability of the nonconformal grid method were assessed from the experimental results and comparative simulation. In conclusion, the flow distribution in the VHTR core was evaluated by the CFD core model with low error and computational cost.