In the safety analysis of high temperature pebble-bed nuclear reactors (PBR), one of the next generation nuclear reactor designs, great computational challenges are presented due to its unique design features. In PBR, tennis ball-sized spherical fuel pebbles are loaded and circulating through the reactor core region under the pressure of high speed helium or fluoride salt coolant flow around each pebble. Interactions of pebble-to-pebble, pebble-to-coolant and pebble-to-reflector wall result in a complicated coupled pebble flow and coolant flow process in PBR. This process is further complicated by the reactor power and temperature distributions, which have strong effect on pebble friction coefficient and coolant flow viscosities. To predict local power and temperature distribution accurately, especially under severe accident scenarios, high fidelity simulation of fully coupled pebble flow and coolant flow in PBR is needed. The development of new methodology used in this high fidelity simulation can significantly improve the current reactor safety prediction capability and provide the safest design margin for PBR.