Molecular dynamics simulation is used to simulate response of nonlinear sinusoidal alternation flow of helium gas oscillation in a pulse tube. Formation of axial pressure wave and temperature field inducted by gas oscillation was studied.Influence of length to diameter ratio on temperature difference and phase of cold and hot ends of the pulse tube is shown. It shows that the pressure wave,speed wave and mass flow wave accompanying by driving force are similar to a sinusoidal function while the temperature wave is similar to a half-sinusoidal function. The oscillation period is shortened with increase of the diameter of the tube and prolonged with increase of the length of the tube. The maximum temperature difference between hot end and cold end increases with the length of the tube but independent of diameter. It is predicted that there is an optimal aspect ratio and oscillation period for pulse tube with different diameter, which increases with increasing of the diameter. It provides a theoretical basis for optimizing efficiency of pulse tube.