A rack cooling system with the pulsating heat pipe and inner duct in data center is suggested and the heat transfer performance is numerically investigated in this paper. The inner structure of the rack is designed and analyzed. The simplified thermal conductivity model of the pulsating heat pipe is introduced in numerical simulation. The temperature of CPUs (Central Processing Units) is evaluated based on the rack electricity power, the working state of the pulsating heat pipe, the temperature of the cooling air and the wind pressure of the rack fans. The results show that the CPUs temperature increases with the rack heating power. The start-up of the pulsating heat pipe (PHP) leads to the temperature of CPUs decrease and the distribution of temperature of CPUs uniformly. The temperature of CPUs decreases with the decrease of the temperature of the cooling air or the increase of wind pressure. The temperature field of the inner air is improved and some “hot spots” are removed by installing an inner duct in the rack. The temperature of CPUs is no more than 60°C in the rack cooling system with load 1380W.