Electrically controlled rotor, also known as swashplateless rotor, represents an active rotor system that, due to the use of a trailing edge flap system instead of a swashplate, not only enables primary control but also conveniently reduces the blade-vortex interaction (BVI) noise of the rotors through active control. The effect of nonharmonic inputs on the control of the BVI noise of electrically controlled rotors based on their unique trailing edge flap systems has been investigated in this paper. To this end, an analytical model for the vortex interaction-induced load and noise of electrically controlled rotor is first established based on the viscous vortex particle method, the Weissinger-L blade model, and the Ffowcs Williams-Hawkings (FW-H) equation. On this basis, a simulation study of flap nonharmonic control for BVI noise reduction in electrically controlled rotors is carried out. According to the mechanism of the BVI in electrically controlled rotors, the second quadrant flap nonharmonic control is used to reduce the advancing side BVI noise, and the effects of different control waveforms and amplitudes on the peak value and directivity of the BVI noise of the sample electrically controlled rotors are analyzed to reveal the noise reduction mechanism of flap nonharmonic control. Subsequently, the effect of the third quadrant flap nonharmonic control on BVI noise on the retreating side of the sample electrically controlled rotors is investigated. The results show that flap nonharmonic control has little effect on miss distance and that it controls BVI noise mainly by reducing the wake vortex strength on the advancing and retreating sides, which may lead to an increase in rotor noise in other regions; the noise reduction effect of flap nonharmonic control for different blade preindex angles indicates that suitable preindex angles coupled with flap nonharmonic control help optimally reduce noise.