The practical operations of rotors for unmanned aircraft systems can undergo time-varying rotation speeds due to various uncertainty factors. This work investigates the aeroacoustic effect of the rotor’s rotation speed fluctuation using both numerical and experimental approaches. The measured real-time angular speed signal reveals that a hovering rotor experiences highly deterministic rotation speed variations in one revolution, which are closely related to the motor property. Delayed detached eddy simulations are performed, and the fluctuating rotation speed is realized by controlling the mesh displacement at each time step. The results suggest that significant additional tones are produced at the excitation frequency and neighbour frequencies, even though the amplitudes of the rotation speed fluctuations at the dominant frequencies are much smaller than the mean rotation speed. By comparing the full signal to individual harmonic components, it is found that the phase difference between each mode is unimportant. Therefore, the total aeroacoustic effect can be regarded as a linear superposition of different harmonic components. Aeroacoustic source analysis is also performed to isolate the contribution of various source types and correlate the far-field noise with the near-field source distribution. The results show that the extra tonal noise is mostly dominated by the loading noise, with a weaker contribution from the thickness noise. The agreement between the experiments and the simulations indicates that the rotation speed fluctuation is likely responsible for the generation of middle-frequency tonal noise at harmonics of the blade passing frequency.