Measuring the catalytical activities of single catalysts in the case of high turnover frequency (TOF, realistic conditions) is highly desirable to accurately evaluate the functional heterogeneities among individuals and to understand the catalytic mechanism. Herein, we report a microwell array-based method to in operando measure the photocatalytic kinetics of single CdS nanoparticles (NPs) with high TOF. This was realized by sealing individual CdS NPs into separated micrometer-sized polydimethylsiloxane wells, thus eliminating the diffusion of products among individuals in the case of high concentration of reactants. This method allowed us to monitor the activities of single catalysts with an average TOF up to 2.1 × 105 s-1. Interestingly, two types of catalytical behaviors were revealed during single CdS photocatalysis: a rapid decline in activity for most CdS NPs and an initial increase in activity followed by a decrease for a minor population of individuals. The developed method will facilitate the investigation of catalytic activities of single particles under realistic conditions and hold great potential in the fields of photo/electro-catalysts, enzymes, functional bacteria, and so on.