Aiming at the difficulty of target tracking for small rotor UAV, a new MHT algorithm considering micro Doppler characteristic is proposed. The micro Doppler characteristic of the UAV is extracted from radar echoes, and the MHT algorithm is used to filter the micro Doppler characteristic whose filtering score is calculated meanwhile. The weighted sum of the micro Doppler characteristic filtering score and the target trace filtering score is used as the final track score for track management. Simulation results show that the tracking stability of the algorithm in this paper is better than the traditional MHT algorithm, the algorithm in this paper reduces the loss of tracking rate from 4.68% of the traditional MHT algorithm to 1.14%, and the position RMS error from about 100m of the traditional MHT algorithm to about 60m.