An electric compressor matching to a free-piston engine generator was optimized using a genetic algorithm and the internal flow characteristics were investigated. The flow losses due to various irreversible factors were quantified by entropy generation analysis. Moreover，the entropy generation and vorticity distribution of the compressor before and after optimization were compared and analyzed to further clarify the optimization strategy. The results show that the ratio of turbulent dissipation，heat transfer dissipation and viscous dissipation in the impeller and diffuser is nearly 6∶3∶1，respectively. Irreversible losses are mainly concentrated in the shroud gap and blade pressure surface. The source of loss is the tip leakage flow with part of the main stream mixed with the reverse vortex. Turbulent dissipation in the volute accounts for more than 85% of the dissipation，specifically in the form of local losses and friction head loss. The isentropic efficiency of the optimized compressor has been increased by 6% and the range and magnitude of the vortex clusters in the flow passages are substantially reduced. The irreversible flow losses are also reduced. The above work reveals the influence of irreversible factors of different dissipation mechanisms on the energy loss and provides guidance for the aerodynamic optimization design of the compressor.