Frequent cyanobacterial blooms pose a serious threat to the aquatic ecosystem and human health, so developing an efficient algae removal method is a long-term goal for bloom management. Current technologies for algal bloom control need urgent improvement in terms of algicide recovery, eco-friendliness and cost. Here we propose a contact-electro-catalytic method, using polytetrafluoroethylene (PTFE) film as a reusable catalyst. This contact-electro-catalytic approach involves the generation of reactive oxygen species (e.g., O2•–, HO•, 1O2 and H2O2) through water-PTFE contact electrification under the low-frequency ultrasonic waves, facilitating the inactivation of algae. The removal rate of the cyanobacterium Microcystis aeruginosa (M. aeruginosa) exposured to the water-PTFE contact-electro-catalytic system is almost five times greater than that of ultrasound alone after 5 h. A mechanistic investigation revealed that the contact-electro-catalytic system damaged the photosynthetic activity, antioxidant system and membrane integrity of the cells. Additionally, LC-MS metabolomic analysis indicated that this system caused substantial significant disruptions in the TCA cycle, amino acid metabolism, purine metabolism and phospholipid metabolism. Three-dimensional fluorescence spectroscopy suggested contact-electro-catalysis could further availably degrade the organic matter. We anticipate that this method can provide an eco-friendly, highly efficient and economic approach for effective control of harmful algal blooms.