The validation of Fire Dynamics Simulator (FDS) was conducted for the under-ventilated fire in well-confined multi-compartments representative of nuclear power plant. Numerical results were compared with experimental data obtained by the OECD/NEA PRISME project. The effects of the numerical boundary conditions (B.C.) in ventilated system and the flame suppression model applied within FDS on the thermal and chemical environments inside the compartment were discussed in details. It was found that numerical B.C. on the vent flow resulting from over-pressure at ignition and under-pressure at extinction should be considered carefully in order to predict accurately the species concentrations rather than temperatures and heat fluxes inside the multi-compartment. The default information of suppression model applied within FDS resulted in artificial phenomena such as flame extinction and re-ignition, and thus the FDS results on the under-ventilated fire showed good agreement with the experimental results as the modified suppression criteria of the fuel used was adopted.