Single-cell analysis of cancer cells is important to improve our understanding of tumor heterogeneity, which could contribute to various clinical applications, such as diagnosis, prognosis, and choice of therapy. In order to improve single-cell analysis throughput, cell-sized microwells in an array are often fabricated and single cells are trapped via various methods such as dielectrophoresis, magnetic and optical techniques. After trapped individually, the cells are either lysed to get intracellular materials or directly analyzed to investigate various intracellular responses to external stimuli. However, besides confinement of each cell in an individual microwell, a real single-cell analysis needs to give individual stimuli to each cell, which prevents the cross-contamination of the intracellular materials among each cell. In this study, we firstly trapped individual cells in cell-sized microwells and obtained a high trapping yield via a dielectrophoresis electrode array. Moreover, an analysis microwell array with photolithographically patterned microgaskets was used for high throughput single cell analysis. The droplets containing stimuli were accurately injected into individual analysis microwells by using an inkjet spotter and the analysis microwells with stimuli were reversibly sealled for liquid tight and were aligned to the trapped cells for single cell analysis. For example, we demonstrated the utility of the developed platform by monitoring the kinetics of calcium fluxes and oscillations in individual Hela cells under the stimulation of drugs. As a universal second messenger in virtually all eukaryotic cells, calcium ions (Ca²⁺) plays a vital role in cellular responses to stimuli and mediates various physiological processes, including neurosecretion, skeletal muscle contraction, cell growth and differentiation. The resulted calcium imaging data revealed significant difference between different cells under the stimulation of drugs. We believe that such a technology will be an essential tool for obtaining high throughput single cell analysis data, in order to indentify statistically significant trends and achieve significant improvements in reagent consumption and analysis time.