With the characteristics of higher refrigeration efficiency, smaller equipment size and applicability in extreme operation condition, gas wave refrigeration technology has been widely used in petrochemical, national defense and other fields. Gas wave refrigerator is based on gas wave motion, which has been studied to some extent. Large eddy simulation is employed to obtain the instantaneous spatial form and numerical distribution of shock wave, expansion wave, and other non-stationary motion in oscillation tube. A three-dimensional large eddy simulation model for the oscillation tube of a double open gas wave refrigerator is established. The characteristics of the dynamic shock wave, expansion wave in the oscillation tube are obtained. For violent oscillation, energy loss is caused during the contact of each nozzle and the oscillation tube especially at the high pressure inlet. The influence mechanism for the energy loss of the operation and structural parameters on the energy transfer efficiency is discussed. The numerical results show that there are strong eddies which lead to turbulent kinetic energy dissipation during the contact process. The energy loss is quantitatively evaluated by the instantaneous turbulent kinetic energy loss ratio. The major instantaneous turbulent kinetic energy loss ratio exists at the vortex core, and increases first and then decreases with the increasing of the absolute pressure ratio and reaches the maximum value of 9.0%, when absolute pressure ratio is 3.61. The instantaneous turbulent kinetic energy loss ratio decreases from 10.7% to 6.0% at the vortex center with the increase of rotational speed from 1100 r/min to 2000 r/min. The instantaneous turbulent kinetic energy loss ratio at the vortex center of the far and the near wall both decrease with the increase of the tube width. The instantaneous turbulent kinetic energy loss ratio at the vortex center of the near wall is larger than that of the far wall, and the difference between the two walls reaches a maximum of 3.2%. The energy transfer efficiency of the gas wave refrigerator could be improved by decreasing absolute pressure ratio, increasing rotational speed and the width of oscillation tube, which also has guiding significance for industrial large flow gas wave refrigerator design.