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In consideration of the high space complexity of the WaveCluster algorithm in the High-dimension, the improved WaveCluster algorithm stored by the cell array is proposed. The clustering analysis is performed with the data got by the rotor fault simulation experiment, the result shows that storing by the cell array can reduce the space complexity of the algorithm and improve the algorithm efficiency. And then the improved WaveCluster algorithm was applied to the rotor fault diagnosis , compared with the other common rotor fault diagnosis method ,the result shows that the rotor fault diagnosis method based on WaveCluster stored by the cell array has the advantages of automatic clustering, high processing speed, high precision and being applicable in high dimensional data space. It can effectively to distinguish the rotor fault state.