The innovative hot stamping press of quenchable steel mainly includes two stages: hot forming of blank at elevated temperature and quenching of hot stamped part in closed water-cooled tools. Crucial stage in hot stamping process is quenching of hot formed part in water-cooled tool to achieve final high ultimate tensile strength. In quenching stage, cooling rate of hot stamped part has a significant effect on final mechanical properties of hot stamped part. Hence, in this paper, a new method is proposed to optimize cooling system to improve effectiveness of quenching and thus final mechanical properties of hot stamped part. In this method, cooling channel is introduced in tools, and hot stamping experiments are combined with corresponding finite element numerical simulations to optimize cooling system. According to cooling system optimization, two different sets of tools used to manufacture square-box-shaped part and B pillar of automobile are manufactured using drilling method and pre-embedding method, respectively. Hot stamping experiments and corresponding simulations are performed to verify the effectiveness of optimized cooling system.