In order to improve the ion transmission efficiency from atmospheric pressure MEMS electrospray (ESI) ion source to mass spectrometry (MS), a novel ion focusing device has been developed and simulated by FEM method (ANSYS). The ion focusing device consists of two electrodes with progressively smaller internal diameters to which electric potential are applied. Taguchi DOE has been used in the optimization process of the structures and critical dimensions for the device. Postprocessing has been implemented by Kriging interpolation method. The shapes of equipotential lines are measured to obtain the response for Taguchi DOE by CAD software. The significance of each factor and optimized structure has been obtained by signal-to-noise (S/N) ratio and means variance analysis. The simulation results will provide good reference for experiments.