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A supersonic separator has been introduced to remove water vapour from natural gas. The mechanisms of the upstream and downstream influences are not well understood for various flow conditions from the wellhead and the back pipelines. We used a computational model to investigate the effect of the inlet and outlet flow conditions on the supersonic separation process. We found that the shock wave was sensitive to the inlet or back pressure compared to the inlet temperature. The shock position shifted forward with a higher inlet or back pressure. It indicated that an increasing inlet pressure declined the pressure recovery capacity. Furthermore, the shock wave moved out of the diffuser when the ratio of the back pressure to the inlet one was greater than 0.75, in which the state of the low pressure and temperature was destroyed, resulting in the re-evaporation of the condensed liquids. Natural gas would be the subsonic flows in the whole supersonic separator, if the mass flow rate was less than the design value, and it could not reach the low pressure and temperature for the condensation and separation of the water vapor. These results suggested a guidance mechanism for natural gas supersonic separation in various flow conditions.