Iron oxide nanoparticles decorated on multi-wall nanotube (MWCNTs) were successfully fabricated through a facile and rapid sonochemical method without any pre-treatment on MWCNTs. FeO/MWCNTs-20 showed a uniform and fine distribution of nanoparticles in the MWCNTs. The obtained FeO/MWCNTs were analysed using TEM and XPS. Notably, FeO/MWCNTs were used for persulfate activation on cyanobacterial cell removal. With 20 mg/L persulfate, FeO/MWCNTs showed an efficient catalytic performance after 1 h treatment. In the FeO/MWCNTs hybrid catalyst, FeO helps to produce sulfate radicals and hydroxyl radicals whereas the size of the FeO clusters could affect the electron transfer for radical generation. Moreover, using high frequency low intensity ultrasound, the combination of persulfate and FeO/MWCNTs-20 reduced the remaining cell number to 9.4% within 30 min treatment. In conclusion, our work demonstrated that low frequency ultrasonic devices are capable of fabricating FeO/MWCNTs via a simple and time-saving route, and the obtained catalysts showed superior catalytic performance on persulfate for harmful cyanobacteria control.