In order to enhance the safety of sodium-cooled fast reactors, a direct reactor auxiliary cooling system (DRACS) under natural circulation conditions with a dipped-type direct heat exchanger (D-DHX) in an upper plenum of the reactor vessel has been investigated. During the DRACS operation, the complicated thermal-hydraulic phenomena that cold coolant from D-DHX flowed into the fuel subassemblies and narrow gaps between them, which is well-known as inter-wrapper flow (IWF) was observed. Therefore, a multi-dimensional thermal-hydraulic analysis model in the reactor vessel for computational fluid dynamics (CFD) code (RV-CFD model) has been developed to evaluate the core cooling performance under natural circulation conditions. For the design study, the RV-CFD model is demanded to simulate with reasonable calculation costs while maintaining accuracy. In this paper, the application of the subchannel analysis method by CFD code for fuel subassemblies (subchannel CFD model) to the RV-CFD model was attempted. In the subchannel CFD model, the porous media approach was used to consider local geometry in the fuel subassembly, and the effective heat conductivity coefficients in diffusion term of the energy equation were set to fit the actual radial thermal diffusion between subchannels. Analysis results were compared to the experimental data obtained in the sodium experimental apparatus PLANDTL-1 and the calculated sodium temperature in the core had good agreement with the experimental result. It was confirmed that the RV-CFD model with subchannel CFD model was applicable to the core thermal-hydraulic analysis during the DRACS with the D-DHX operation under natural circulation conditions.