Pulse detonation engines (PDEs) with three different types of nozzle–straight ejector combinational structures at three different ejector positions were simulated by the unsteady 2-D axisymmetric method to understand the influence of nozzle–ejector combinational structures on the performance of PDEs. Three types of nozzles included the straight nozzle, convergent nozzle, and convergent–divergent (CD) nozzle. Three ejector positions were considered according to the ratio of the distance between the nozzle outlet and the ejector inlet to the diameter of PDEs (Δx/d). Propane was used as the fuel and air as the oxidizer. The simulation results indicated that for the PDE with the straight nozzle, it took the shortest time for high-temperature burnt gas to exhaust from the detonation tube. For the PDE with the CD nozzle, the time at which the ejector was filled with external air was the fastest. Within the time range of t = 0–10 ms, the ejected air was less than the original air in the ejector among all the nine combinational structures. The maximum ejected air was obtained with the convergent nozzle, followed by the CD nozzle, and the minimum with the straight nozzle. For certain nozzles, the maximum air was ejected at the ejector position of Δx/d = +1, followed by the ejector position of Δx/d = 0, and the minimum at the ejector position of Δx/d = −1. For the convergent nozzle–ejector combinational structure, the air ejection speed was the fastest. Oxygen concentration distribution in the PDE with the CD nozzle was more uniform along the axial direction than the other nozzles.