Despite the increased attention that has been given to the unmanned aerial vehicle (UAV)-based magnetic survey systems in the past decade, the processing of UAV magnetic data is still a tough task. In this paper, we propose a novel noise reduction method of UAV magnetic data based on complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN), permutation entropy (PE), correlation coefficient and wavelet threshold denoising. The original signal is first decomposed into several intrinsic mode functions (IMFs) by CEEMDAN, and the PE of each IMF is calculated. Second, IMFs are divided into four categories according to the quartiles of PE, namely, noise IMFs, noise-dominant IMFs, signal-dominant IMFs, and signal IMFs. Then the noise IMFs are removed, and correlation coefficients are used to identify the real signal-dominant IMFs. Finally, the wavelet threshold denoising is applied to the real signal-dominant IMFs, the denoised signal can be obtained by combining the signal IMFs and the denoised IMFs. Both synthetic and field experiments are conducted to verify the effectiveness of the proposed method. The results show that the proposed method can eliminate the interference to a great extent, which lays a foundation for the further interpretation of UAV magnetic data.