Large separate heat pipe is a potential selection to establish the passive cooling system to remove decay heat from the Spent Fuel Pool. In this system, heat pipes are expected to work properly and effectively for a long time without human intervention. Due to the physical dimensions and structures, flow patterns, and fluid distribution in large‐scale heat pipes differ from those in conventional ones. Based on the condensation flow patterns, a flow condensation model is presented. Then, a separate heat pipe model considering filling ratio effects is developed. Using the new model, the mean absolute errors of simulation are 5.5% (water), 5.1% (ammonia), and 4.3% (R134a). While in the conventional condensation model, these errors are 29.4%, 9.7%, and 10%. It is found that the influence of filling ratio varies with working fluids. For water heat pipe, the optimal filling ratio is about 17%. Higher or lower filling ratios lead to degradation of heat transfer capacity. For R134a or ammonia, the optimal filling ratio is a range, about 20% to 70%. The boundary of the range relates to both evaporator outlet vapor quality and heat pipe downcomer liquid column height.