In this study, the effect of changing the diameter of the vortex finder, cone and hydraulic inlet diameter of the cyclone under oscillating flow conditions is compared to under uniform flow. In using cyclones as an inlet air filter for the internal combustion engine, the cyclone flow cannot be considered ideally uniform, and flow oscillations must be applied to the boundaries. Also, optimizing the dimensions of the cyclone can provide the necessary space for other uses in the engine space. Numerical solution validation has been performed and seven cyclone models have been created. Then, the effect of geometry variation on the flow field is investigated by examining the frequency and power of active vortices in the vortex finder, cylinder and cone zones. Also, the cyclone performance parameters, including Euler number and efficiency, have been investigated for different models, and correlations have been proposed to estimate them under non-uniform flow. Multi-objective optimization is performed using the genetic algorithm for introducing the most optimal cyclone geometry. Under non-uniform flow conditions, increasing the vortex finder and cone diameter by 50% and decreasing the hydraulic inlet diameter by 40% reduce the Euler's number by 52 to 62%.