Abstract: Pulse tube refrigerator is widely used in many fields,but there is a lack of research on the influencing factors of the gas thermodynamic characteristics in the pulse tube.In this paper,three different types of channels were established using molecular dynamics methods.The thermodynamic process of gas flow inside the pulse tube was simulated.The effects of wall roughness and channel shape on the temperature field of gas flow in the pulse tube was studied.The simulation results show that as the height of the roughness increases,the heat caused by friction make the temperature increase;the friction caused by the shape of the channel also leads to the temperature increase.Both are not facilitate the cold end refrigeration.The effect of rough elements on the cold end temperature is more than the channel shape.The system pressure also affects the cold end temperature.As the system pressure increases,the cold end temperature decreases.