In order to purify rotor orbit，the characteristics of suppressing the phenomenon of mode mixing and filtering in ensemble empirical mode decomposition (EEMD) are studied，and a method of rotor orbit purification is presented. Ensemble empirical mode decomposition decomposes a complicated signal into a collection of intrinsic mode functions (IMFs). Then，according to prior knowledge of rotor system，choose intrinsic mode function components and reconstruct the signal，and，the purification of rotor orbit is obtained. The effectiveness of the method is proved by the successful purification of rotor orbit coming from the test-bed. And，the results of comparing the performances of the proposed method to the harmonic-based and the EMD-based purification of axis orbit method show the advantage of the de-noising method. The method provides a new way for fault diagnosis of rotating machinery.