Stratification behavior is of great significance in the late in-vessel stage of core melt severe accident of a nuclear reactor. Conventional numerical methods have difficulties in analyzing stratification process accompanying with free surface without depending on empirical correlations. The Moving Particle Semi-implicit (MPS) method, which calculates free surface and multiphase flow without empirical equations, is applicable for analyzing the stratification behavior of fluids. In the present study, the original MPS method was improved to simulate the stratification behavior of two immiscible fluids. The improved MPS method was validated through simulating classical dam break problem. Then, the stratification processes of two fluid columns and injected fluid were investigated through experiments and simulations, using silicone oil and salt water as the simulant materials. The effects of fluid viscosity and density difference on stratification behavior were also sensitively investigated by simulations. Typical fluid configurations at various parametric and geometrical conditions were observed and well predicted by improved MPS method.