To solve the modal mixing problem of EMD in the applications of harmonic detection, this paper analyzes the problem combined with the boundedness of EMD in the decomposition process and the practical situation of harmonic detection. Firstly, this paper uses the EEMD method to eliminate the modal mixing problem caused by the interference of intermittent signal. Secondly, aiming at the mixing problem of dense frequency signal, it proposes the EEMD harmonic detection method based on the frequency shift of Hilbert. This method decomposes harmonic signal in EEMD, and then uses the correlation to judge whether it is mixed with close signals. If there is the modal mixing problem, it will use the frequency shift of Hilbert to make the signal satisfy the decomposition condition of EEMD, thus decompose the complex signal into many single signals. The simulation verifies that the method can effectively overcome the problems caused by the interference of intermittent signal and dense frequency signal in the harmonic detection and meanwhile insure the effective decomposition and the practicability. The analysis of the actual rectified signal proves that the method has a good detection result.