Abstract The complex geometry of the hexagonal fuel blocks of the prismatic fuel assembly in a very high temperature reactor (VHTR) hinders accurate evaluations of the temperature profile within the fuel assembly without elaborate numerical calculations. Therefore, simplified models such as a unit cell model have been widely applied for the analyses and designs of prismatic VHTRs since they have been considered as effective approaches reducing the computational efforts. In a prismatic VHTR, however, the simplified models cannot consider a heat transfer within a fuel assembly as well as a coolant flow through a bypass gap between the fuel assemblies, which may significantly affect the maximum fuel temperature. In this paper, a three-dimensional computational fluid dynamics (CFD) analysis has been carried out on a typical fuel assembly of a prismatic VHTR. Thermal behaviours and heat transfer within the fuel assembly are intensively investigated using the CFD solutions. In addition, the accuracy of the unit cell approach is assessed against the CFD solutions. Two example situations are illustrated to demonstrate the deficiency of the unit cell model caused by neglecting the effects of the bypass gap flow and the radial power distribution within the fuel assembly.