Abstract: In the hypersonic test facilities driven by free piston compressors, the operation condition of the free piston compressor is conclusive to the status of the test gas, the effective test time and the facility safety. Based on the structural parameters of FD-21 free piston shock tunnel and the typical operation condition of the free piston compressor, quasi-one-dimensional simulation and isentropic theoretical prediction of the flow in the compression tube were conducted, and the complex wave structures as well as the changes of the flow parameters induced by the non-isentropic effect were analyzed. The source of the entropy change in the compression tube was attributed to two mechanisms: the shock wave and the viscosity. Through the transverse comparison of simulation results with the variation of driving pressure, piston mass, initial pressure in the compression tube and compression tube length, the entropy change attributed to each mechanism was normalized with piston compressor operation parameters, and a unified entropy change formula was obtained. Finally, the isentropic model of piston compressor operation was modified with the entropy change profile, and better agreement with experimental and numerical results was acquired.