The harmonic detection method based on Complementary Ensemble Empirical Mode Decomposition (CEEMD) is susceptible to the interference of iterations and auxiliary white noise, resulting in the defects of false component and mode mixing. And CEEMD method has the defect of low precision in detecting harmonic signal under noise background. To solve the above problems, a new PE-CEEMD harmonic detection method was proposed based on the combination of Permutation Entropy (PE) algorithm and CEEMD. Firstly, the harmonic signal is decomposed by CEEMD to obtain a series of Intrinsic mode-functions (IMF) with frequency from high to low. The PE algorithm was used to quickly select and eliminate the noise components with large randomness, and then CEEMD decomposition was performed for the remaining signals. Simulation results show that PE-CEEMD method can overcome the problems of modal aliasing and false components better than CEEMD method, and the detection accuracy of frequency components and amplitude of complex harmonic signals is improved by 4.424% and 9.3%, respectively.