The tube inside and outside heat transfer mechanism of Passive Residual Heat Removal Heat Exchanger (PRHR HX) was analyzed. The calculation method of this special heat exchanger under natural convection condition in In-containment Refueling Water Storage Tank (IRWST) was carried out. The single-tube coupling model three-dimensional natural circulation in the IRWST was simulated numerically using Fluent. The heat transfer and flow characteristics of the fluid in IRWST were obtained. The comparison of the results between theoretical arithmetic and numerical simulation showed that the theoretical calculation method is suitable for the heat transfer calculation of PRHR HX.