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