Using the excess energy of a high-pressure fluid to pressurize a low-pressure fluid for achieving full utilization of pressure energy satisfies the energy-saving, low-carbon, and environmentally-friendly process engineering requirements at present. Therefore, the gas wave ejector (GWE) has a wide range of applications in many industrial processes as a device that can efficiently realize the above-mentioned comprehensive energy utilization process. Because GWE transfers energy through pressure waves formed during the connecting and closing of wave rotor passages to the pressure ports, the proper design of pressure ports distribution positions is the precondition for the device's efficient operation. The design method of pressure ports based on the wave system theory is described, and the influence mechanism of port positions on equipment performance is determined using a combination of three-dimensional numerical simulation and experiment. The results suggest that the equipment performance can reach the optimal value once the port positions satisfy the design method. However, when the port position deviates from the design values, the emergence of adverse effects such as backflow of medium-pressure gas and insufficient low-pressure gas intake result in the equipment performance declining. Due to the different impact mechanisms of different port positions on performance, the function degradation caused by port location deviation is also different. The following four conditions can lead to significant performance degradation: opening the medium-pressure port too late or closing it too early, and opening the low-pressure port too late or closing it too early. These situations should be avoided during GWE design and manufacturing. The presented research results enrich the parameters design theory of GWE, and have important guiding significance for the research and application of this equipment.