The gas wave rotor was usually designed and performed on the ideal gas model. However, the real gas effect could not be ignored anymore under high-pressure ratio conditions. In this study, for the first time, a two-dimensional computational model of a double-opening gas wave refrigerator (GWR) using a multi-parameter Benedict–Webb–Rubin equation of state is established and the influence of the real gas effect on gas wave dynamics and energy transfer processes in the GWR with discontinuous boundary conditions is thoroughly investigated. The numerical results show that the wave dynamics of the ideal gas and the real gas are similar under different operating conditions, but compression waves and expansion waves in real gas obviously lag behind the ideal gas. In addition, the low-temperature real gas is completely discharged earlier than the ideal gas and the difference between them gradually increases as the pressure ratio gets higher, which benefits the GWR compact structure design and cost reduction. At the same time, the temperature of the real gas being discharged is lower than that of the ideal gas. Therefore, the refrigeration efficiency of the isentropic expansion of the real gas will be improved compared with the operation in ideal gas. The research results on the real gas effect reveal the mechanism of wave dynamics and energy transfer, providing support for the optimization design of GWR.