Electroporation, is widely used method that can be directly applied to the field of gene therapy. However, very little is known about the basic mechanisms of DNA transfer and cell response to the electric pulse. As a more convenient and effective tool for the investigation on the mechanisms of electroporation and the enhancement of the functional efficiency, we developed a micro-electroporation chip with polydimethylsiloxane (PDMS). Owing to the transparency of PDMS, we could observe the process of Propidium Iodide (PI) uptake in real-time, which shows promise in visualization of gene activity in living cells. Furthermore, the design of the electroporation chip as a microchannel offers advantages in terms of efficiency in permeabilization of PI into SK-OV-3 cells. We also noticed the geometric effect on the degree of electroporation in microchannels with diverse channel width, which shows that the geometry can be another parameter to be considered for the electroporation when it is performed in microchannels.