In this study, for the purpose of the optimization of the measurement system performance, a three-dimensional numerical model of the particle charge and size analyzer (PCSA) is presented. The PCSA is capable of simultaneous particle size and charge measurement using phase Doppler anemometry. Numerical simulations of particle transport under the influence of the square-wave excitation field have been carried out to identify the optimal PCSA system configurations, improve the particle detection rate, and minimize the measurement bias due to experimental conditions. For the first time, the threedimensional (3-D) numerical model was used to study the effects of excitation frequency, magnitude of the electric field, and particle inlet velocity on the particle detection rate and charge and size measurement bias. The airflow and the particle motion in the measurement cell were investigated using commercial FLUENT 14.5 software and the particle detection and validation algorithm was implemented in MATLAB. The particle phase was modelled using the Lagrangian approach. The effect of the electric field on particle trajectories was analyzed by solving a coupled system of the electric field and particle transport equations using the User-Defined-Functions (UDFs) in FLUENT. The model was validated by comparing the numerical results with reported experimental data. This 3-D numerical simulation provides a valuable insight into various tradeoffs between the detection rate of particles with different electrical mobility levels and the PCSA parameters. The numerical simulation results demonstrate that the reduction of the measurement bias of particle charge and size distribution can be achieved while maintaining high particle detection percentage by an appropriate selection of system parameters, leading to a more representative profile of measured aerosols. It is shown that the optimal ranges of the excitation frequency, magnitude of electric field, and particle velocity at inlet are between 40 - 50 Hz, 0.3 - 0.4 MV/m, and 0.01 - 0.03 m/s, respectively.