The pebble bed water-cooled reactor (PBWR) provides another prospective energy source with advantages of traditional pressurized water reactor (PWR) and pebble bed reactor (PBR). Nevertheless, researches on PBWR are too scarce to advance its further development. This research investigates the thermal hydraulics of body-centered cubic (BCC) and face-centered cubic (FCC) PBWR core through computational fluid dynamics (CFD). Bridge model is adopted to modify the contact points between adjacent pebbles, thus making it possible to generate high quality meshes in narrow spaces. The comparison between BCC and FCC arrangement is conducted to analyze their influence on water flow and heat transfer. Results indicate that the average value of Nusselt number ( Nu )for BCC arrangement is 50% lower than FCC arrangement, whereas the pressure drop coefficient for FCC arrangement is 4.4 times as that of BCC arrangement. Furthermore, vortices are identified in void space for both arrangements but their contribution to improving heat transfer is different. In addition, the maximum temperature of fuel pebbles for both arrangements is about 1400K lower than melting point of Zirconium. Last, the simulation results are compared to KTA, which shows good correspondence generally.