A three-dimensional thermal-hydraulic model has been built to numerically simulate the flow and heat transfer in a 5 MW integral nuclear heating reactor (NHR-5). The simulation is performed with the general purpose commercial CFD code PHOENICS. The porous media model has been used to model the complex structure in the core and heat exchangers. The numerical model is validated by the asymmetric operation test results of the NHR-5. A comparison of the simulation results with the test results shows a good agreement. Analyses also show that shutting down half of the main heat exchangers in the NHR-5 will result in neither significant asymmetric distributions of the system parameters in the core nor a deterioration of reactor safety.