A noise covariance matrix (NCM) estimation method for unmanned aerial vehicle (UAV) audition is proposed with rotor noise reduction as its primary focus. The proposed NCM estimation method could be incorporated into audio processing algorithms using UAV-mounted microphone array systems. The NCM is formed through accurate estimation of the microphone array input signal's amplitude and phase by using a multi-sensory rotor noise power spectral density (PSD) estimator and a filter formed by exploiting the acoustical relationship between the microphone array and the rotor noise sources, respectively. The estimated NCM aims to be readily incorporable into several source enhancement algorithms to reduce the effects of rotor noise and improve the resultant audio quality. Experiment evaluation using real in-flight UAV rotor noise recordings shows that the estimated NCM significantly improves rotor noise reduction (of up to$\sim 28$dB) and the quality of the target sound.