Abstract Passive residual heat removal heat exchanger (PRHR HX) is a key equipment in advanced passive safety pressurized water reactors (PWRs), such as AP1000. Immerged in the In-containment refueling water storage tank (IRWST), the C-shape PRHR HX removes the residual heat using natural convection and boiling heat transfer during postulated accidents. Therefore, the safety operation of the PRHR HX is very important for the nuclear power plant (NPP). In this paper, three dimensional CFD simulation of the secondary side fluid flow and heat transfer of the PRHR HX is performed. The drift flux model is used to simulate the two phase flow phenomenon in the IRWST. The tube region is modeled by the porous media approach. The flow resistance in the tube region is calculated by empirical pressure drop correlation and two phase flow multiplier. The heat transfer rate from the primary side to the secondary side fluid is also evaluated by widely used heat transfer empirical correlations. Additional source terms corresponding to the flow resistance and removed heat in the tube region are added to the momentum and energy equation, respectively. The governing equations are solved by the commercial CFD package FLUENT. Three dimensional distributions of the fluid velocity, temperature and void fraction are obtained. The heat transfer characteristics of the tube bundle is analyzed.