The cellular heterogeneity and plasticity are often overlooked due to the averaged bulk assay in conventional methods. Optical imaging-based single-cell analysis usually requires specific labeling of target molecules inside or on the surface of the cell membrane, interfering with the physiological homeostasis of the cell. Scanning electrochemical microscopy (SECM), as an alternative approach, enables label-free imaging of single cells, which still confronts the challenge that the long-time scanning process is not feasible for large-scale analysis at the single-cell level. Herein, we developed a methodology combining a programmable SECM (P-SECM) with an addressable microwell array, which dramatically shortened the time consumption for the topography detection of the micropits array occupied by the polystyrene beads as well as the evaluation of alkaline phosphatase (ALP) activity of the 82 single cells compared with the traditional SECM imaging. This new arithmetic was based on the line scanning approach, enabling analysis of over 900 microwells within 1.2 h, which is 10 times faster than conventional SECM imaging. By implementing this configuration with the dual-mediator-based voltage-switching (VSM) mode, we investigated the activity of ALP, a promising marker for cancer stem cells, in hundreds of tumor and stromal cells on a single microwell device. The results discovered that not only a higher ALP activity is presented in cancer cells but also the heterogeneous distribution of kinetic constant (kf value) of ALP activity can be obtained at the single-cell level. By directly relating large numbers of addressed cells on the scalable microfluidic device to the deterministic routing of the above SECM tip, our platform holds potential as a high-content screening tool for label-free single-cell analysis.