Electroporation serves as a powerful technique to introduce the exogenous nucleotides, DNA, RNA, proteins, dyes, and virus particles into cells. Through the effect of high intensity of electric field, the permeability of the cell membrane is instantaneously improved to absorb the exogenous molecules in surrounding medium. To protect the cell viability, ultralow-voltage electroporation techniques are well developed by versatile devices, and delivery efficiency is commonly assessed by label-based analysis by microscope-ImageJ or flow cytometry. However, accuracy and complexity of these analytical strategies still hinder efficient and precise biomedical studies in situ. Here we developed an intracellular delivery biosensing system by nanostrawed electroporation array (NEA) that can efficiently assess the universal electroporation performance by cell viability, delivery efficiency, and cell mortality. The intracellular delivery biosensing system consists of NEA, fluorescent microscope, and automated analysis software. Intracellular delivery biosensing system of electroporation quality is based on the enhanced fluorescent watershed segmentation (enhanced FWS) algorithm, which possessed low deviation (~5%) and significantly shortened the operation time (~8 s/10 images) in contrast to high deviation (~13%) and long operation time (~10 min/10 images) of conventional inaccurate, labor-intensive and time-consuming methods. It is believed that the intracellular delivery biosensing system will be a promising universal platform to assess nanodevice electroporation in the fields of cell biology, biotechnology, and medicine.