In this paper, computational fluid dynamics (CFD) gas flow simulations are carried out for the pebble bed reactor. In CFD calculations, geometry modeling and physical modeling are crucial to CFD results. The effects of the treatments of the interpebble contacts on gas flow fields and heat transfer are examined. A sensitivity analysis for the gap size is conducted with two spherical pebbles, in which the interpebble region is modeled by means of two types of interpebble gap and two kinds of direct contact. Both large eddy simulation and Reynolds-averaged Navier–Stokes models are employed to investigate the turbulent effects. It is found that the flow fields and relevant heat transfer are significantly dependent on the modeling of the interpebble region. The calculations indicate the complex flow structures present within the voids between the fuel pebbles.