Compliant foil gas seal technology is one of the advanced non-contact cylindrical gas film seal technology. Under extreme operation parameters, including high boundary velocity, high differential pressure, high vibration and high temperature, the compliant foil gas seal can meet the requirements of high performance rotary machines. However, there is less research on the dynamic signal characteristics mechanism of compliant foil gas seal technology with different surface roughness running. Therefore, the acoustic emission signal characteristics with different surface roughness were collected from acoustic emission source of gas seal rig, which was firstly constructed. Then, the acoustic emission signal characteristics with different surface roughness were extracted and further discussed by making use of the waveform diagram and Fast Fourier Transform. The acoustic emission frequency characteristics were applied and analyzed with the variation of different surface roughness, differential pressure, boundary velocity and film thickness, in order to obtain the information of the amplitude frequency and acoustic emission frequency characteristics. The results showed that the frequency characteristics of acoustic emission signal on different surface characteristics were significantly different, especially in the surface roughness. In addition, there were obviously at least two center frequency distribution of the acoustic emission signal characteristics of compliant foil gas seal system. The phenomenon was probably caused by the variation of the wedge gap structure of cylindrical structure gas seal, which was the operating principle of compliant foil gas seal. Furthermore, with the variation of the differential pressure and velocity in this paper, the acoustic emission frequency distribution changed, but the acoustic emission center frequency distribution hardly changed. Finally, the frequency distribution of acoustic emission signal characteristics with same surface roughness of the film thickness was different. It was on account of the rapidly decrease of high frequency characteristics with the increase of film thickness.