We describe a miniature high-voltage power supply (HVPS) with dimensions of 4.7 x 5.6 x 2.5 cm (W x L x H) powered by universal serial bus (USB) ports. Two strategies were adopted to ensure its efficient power usage. (i) Only two high-voltage converters (one positive and one negative) and two relays were used for power saving, while keeping the sample plug stable and well-defined and avoiding sample leakage for microchip electrophoresis. (ii) The components and their running modes were specially designed to decrease power waste according to the feature of different periods of the microchip electrophoresis process. Performance of this USB-based mini-HVPS was demonstrated using sodium fluorescein analyte with microchip electrophoresis/LIF detection.