This paper describes the computational fluid dynamics (CFD) analysis and validation works from the previous experimental study on the natural convection driven by outer surface cooling in the presence of density stratification consisting of air and helium (as a mimic gas of hydrogen). The experiment was conducted in the Containment InteGral effects Measurement Apparatus (CIGMA) facility at Japan Atomic Energy Agency (JAEA). CIGMA vessel is a large cylindrical stainless steel with an inner diameter of the main cylindrical part 2.5 m and an overall height of 11 m. The mass fraction proportion of helium in the whole vessel was 11% and the helium molar fraction at the top vessel was 48%. Two experiments were performed and the numerical simulation was carried out to analyze the detailed effect of the cooling region on the erosion of the helium stratification layer. First test was named CCLP30 or case 1 and second test was named CCPL34 or case 2. The main difference between case 1 and case 2 was the cooling area of case 1 was narrower than case 2. In case 1, cooling area was only located at the one-fourth of outer vessel. Whereas, in case 2, cooling area was located at one-half of outer vessel. The temporal and spatial evolution of the helium concentration and the gas temperature inside the containment vessel was predicted and validated against the experimental data. The results indicated that the numerical predictions fairly agreed with the experimental data. However, the predicted erosion rate showed discrepancies compare with the experimental data. The relative errors time required for the complete dissolution of the helium gas were within 15%. In addition, two stratification behaviors that depend on the cooling location were presented and discussed. The CFD simulation confirmed that an upper head cooling caused two counter-rotating vortexes in the helium-rich zone. Meanwhile, the upper half body cooling caused two counter-rotating vortexes in the helium-poor zone. These findings are important to understand the mechanism of the density stratification process driven by natural convection in the containment vessel.