It is one of the critical issues to understand heat transfer characteristic of the pulse tube in developing a more efficient pulse tube refrigerator at cryogenic temperature. This paper describes the experimental investigation on the heat transfer mechanism during both oscillating pressure and oscillating flow. The gas temperature ami the tube wall temperature along the pulse tube were measured with fast response thermocouples for various cycle conditions. The real time measurement of the heat flux using the heat flux transducers was also made at the warm and the cold end heat exchangers. The pressurization period of a pulse cycle was varied by controlling the stepper motor in the rotary valve system to study the effect of pressure wave shape. The phase difference between the heat flux and the temperature difference was clearly observed. The cyclic mean Nusselt number for the several cyclic frequency was calculated. To improve the heat-pumping characteristic of the pulse tube refrigerator, a unique design of the warm end heat exchanger was also proposed.