This paper describes and characterizes an electroporation microchip device and system optimization. This device combines microfabrication techniques, logic circuit, and electrophoresis design to create a multi-function gene transfection device that can be used in a number of medical science research applications. This device consists of two components: a cell-accommodation cavity and electrodes for providing electroporation and electrophoresis electric power. We demonstrated the ability to use electrophoresis force to increase the gene concentration on site-specific surface of cell lines which further enhanced the gene delivery. Meanwhile, the parameters of the electroporation system, which could have an influence on the delivery rate, were optimized by the Taguchi method, resulting in optimized values of 50 μm electrode gap, 80 μg/mL pEGFP-N1 concentration, 6 V applied transfection voltage, and 2-pulse per time with above 95 % confidence. Experimental results showed that the efficiency of gene transfection with an attracting-electric field become much higher than that without an attracting-electric field, and the delivery rate was up to 35.89 % when utilizing GEP genes into NIH-3T3 cells. The electrostatic force can be designed into specific regions, where the DNA plasmids are attracted to provide the region-targeting function. The adherent cells could be manipulated in situ without detachment by this electroporation microchip. The system has several advantages of portable, cost-effective, high transfection rate and easy operation.