It is of great significance to detect drones in airspace due to the substantial increase and regrettable misuse in the consumer market. In this paper, we establish a micro-motion theoretical model of a drone and analyze the micro-Doppler signature of rotor targets and the flicker mechanisms of the multi-rotor targets. Hence, for the target recognition problem of multi-rotor drones, a multi-rotor target micro-Doppler parameter estimation method is proposed. Firstly, a signal frequency domain segmentation method is proposed based on the complex variational mode decomposition (CVMD) to separate the high-frequency part of the high-frequency flicker in the frequency domain. Secondly, for the signal after frequency domain segmentation, a flicker time domain position method based on singular value decomposition (SVD) is proposed. Finally, by integrating CVMD frequency domain segmentation and SVD time domain positioning, the reconstruction of multi-rotor target scintillation at different speeds is realized, and the micro-motion parameters of rotor blades are successfully estimated. The simulation results show that the method has high accuracy in estimating the micro-motion parameters of a multi-rotor, which makes up for the shortage of the traditional method in estimating the micro-motion parameters of the multi-rotor target.