The high throughput particle separation system includes an aqueous solution container for storing an aqueous solution containing specific particles to be separated, an electrode array, having a plurality of electrodes arranged at regular intervals or at various different intervals in series or in parallel, for deflecting specific particles simultaneously in a nonuniform electric field according to sizes and dielectric properties of the particles to separate a large quantity of the particles at high throughput, a path separation unit for establishing movement paths of the particles separated by the electrode array, and a control unit for applying the same voltage and frequency or different voltages and frequencies to the electrodes of the electrode array based on sizes and dielectric properties of specific particles to be separated.