The ability to precisely deliver molecules into single cells while maintaining good cell viability is of great importance to applications in therapeutics, diagnostics, and drug delivery as it is an advancement toward the promise of personalized medicine. This paper reports a single-cell individualized electroporation method with real-time impedance monitoring to improve cell perforation efficiency and cell viability using a microelectrode array chip. The microchip contains a plurality of sextupole-electrode units patterned in an array, which are used to perform in situ electroporation and real-time impedance monitoring on single cells. The dynamic recovery processes of single cells under electroporation are tracked in real time via impedance measurement, which provide detailed transient cell states and facilitate understanding the whole recovery process at the level of single cells. We define single-cell impedance indicators to characterize cell perforation efficiency and cell viability, which are used to optimize electroporation. By applying the proposed electroporation method to different cell lines, including human cancer cell lines and normal human cell lines individually, optimum stimuli are determined for these cells, by which high transfection levels of enhanced green fluorescent protein (EGFP) plasmid into cells are achieved. The results validate the effectiveness of the proposed single-cell individualized electroporation/transfection method and demonstrate promising potential in applications of cell reprogramming, induced pluripotent stem cells, adoptive cell therapy, and intracellular drug delivery technology.