Natural circulation is the important way for taking away decay heat in pool-type sodium-cooled fast reactor (SFR) when all primary pumps trip. Three-dimensional (3D) unrestricted flow and thermal stratification phenomena exist in sodium pool during natural circulation. 3D modeling of whole reactor system with complex secondary or third circuit may generate huge numbers of grid, it may cause the difficulty of performing simulation. 3D computational fluid dynamics (CFD) method is mainly used for the thermal hydraulic analysis in primary system. The power variation of heat exchanger is unclear under natural circulation condition, which is key boundary condition in 3D CFD simulation. It is necessary to develop the numerical method for realizing the boundary more closed to the actual condition. In this paper, a “1D system code + 3D CFD” simulation method combining the simulation of 3D CFD and system code SAC-IRACS was proposed. The steady and transient simulations with 24000 s of PHENIX natural circulation test were performed. Flow paths in PHENIX primary system during the test were identified and mass flow rate were obtained. 3D thermal stratification phenomena in sodium pool during natural circulation test were captured. Variation trends of key thermal hydraulic parameters are basically consistent with the test. There is the reverse flow in RVCS under natural circulation conditions. At 24000 s, mass flow rate of reactor core, primary pumps and RVCS are 63.13 kg/s, 58.04 kg/s, −5.11 kg/s respectively. The decay heat in primary system can be taken away by intermediate reactor auxiliary cooling system (IRACS). Obvious thermal stratification phenomena appear again in sodium pool with the efficient cooling. This “1D system code + 3D CFD” simulation can provide reasonable results, and can be applied to natural circulation analysis in other pool-type SFRs.