The frequent outbreak and continuous expansion of harmful cyanobacteria blooms (HCBs) have become important environmental concerns and public health issues globally. In this study, the “micron-confined Fe(II)-modified-microcapturer (FMC)-triggered Fenton” technology was established as advanced process adaptable to the HCB treatment. Results show that 95.7–99.4% of cyanobacteria cells were captured and separated from the HCB water at the optimum doses of Fe(II) and H2O2 within only 30 s. The chain-like cyanobacteria of A. flos-aquae were easier to be collected by FMCs compared with the unicellular M. aeruginosa. It was confirmed by scanning electron microscopic observation and fluorescence staining flow cytometry measurement that the FMC-carrying Fe(II) played the roles of both cell-gripper and Fenton catalyst. During the one-step process, the FMC-triggered Fenton effectively inhibited the cyanobacteria regrowth via inactivating the cells, and meanwhile, the microcystins of LR and RR were removed. The analyses by continuous flow chemiluminescence and X-ray photoelectron spectroscopy denote that FMCs performed efficiently in capture and Fe(II)-catalytic oxidation through increasing mass transfer, exposing sufficient active reactive oxygen species active-sites on the FMC surface and accelerating electron transfer. The micron-field-confined cascade processes retained the robust performance of Fenton against the high pH of bulk HCB water. This novel interface-dependent Fenton method is a promising tool for HCB treatment owing to its great efficiency, versatility, rapidness and eco-environmental friendliness.