Single-atom catalysts exhibit the excellent catalytic activity and selectivity, making them widely applicable in the fields of advanced materials, environmental science, and chemical synthesis. However, understanding the mechanism of single-atom catalytic reactions, such as the hydrogen generation reaction, is still challenging, which notably hampers the optimization and precise control of the reaction. Here, we immobilize a single-metal atom model catalyst into a single-molecule electrical detection platform for in situ monitoring of the catalytic hydrogen generation process at the single-event level. In combination with theoretical and experimental studies, the catalytic mechanisms of the hydrogen generation reaction, especially the selection of the catalytic center through charge, spin, and orbital quantum control, are elucidated. In addition, a hydrogen generation process via quantum spin-induced catalysis is observed, in which the turnover frequency increases by about 65 times at a magnetic field of 50 mT. This study provides valuable insights into the intrinsic mechanism of single-metal atom catalysis and opens up unique avenues for their precise control, thus offering a useful strategy for efficiently developing clean energy.