Ejector is an important device to improve the efficiency of thermal seawater desalination system. In this work, the internal flow and transport characteristics of a two-stage ejector are investigated via a three-dimensional numerical simulation. The mixing and diffusion processes of ejecting and working fluids are also analyzed to identify the factors related to energy consumption. The simulation results showed that, the maximum velocity of the ejector occurs in the axis direction and the streamline distribution in the nozzle and mixing chamber is uniform. However, one or multiple vortices are generated in the suction chamber, which causes the uneven distribution of streamline. The negative pressure at the entrance of the suction chamber increases firstly, and then decreases with the increasing velocity. The amount of vortex decreases with increasing velocity, which helps to improve the efficiency of ejector. Vortex dissipates faster with increased distance from the central line and the turbulent dissipation increases significantly, which results in a rapid dissipation of vortex.