Supersonic cyclone separator is a novel type of natural gas dewatering device that overcomes the shortcomings of traditional dewatering methods. In order to investigate the factors affecting the separation efficiency and improve the separation performance of the supersonic cyclone separator, the discrete particle model was employed in numerical calculation. On the basis of an accurate numerical model, the flow field of supersonic cyclone separator was analyzed, the trajectories of droplets were predicted, and the factors affecting the separation efficiency of droplets were investigated. The numerical results indicated that Laval nozzle could provide the necessary conditions for the condensation of water vapor. The swirler can throw droplets onto the wall or into the separator, both of which are foundations for realizing the separation of droplets. Droplets had three typical trajectories affected by centrifugal effect and inertia effect. The existence of a shock wave increases the swirl intensity of droplets, which is conducive to the separation of droplets. The diameter of droplets should be increased as much as possible in order to improve separation efficiency, and the gas–liquid area ratio should be about 45.25%, and the number of vanes should be 10.