Abstract: In this paper, a new local alignment algorithm based on Qmax is proposed to identify the cover versions. By changing the step size condition, the proposed algorithm can prevent the generating of pathological warping and improve the final score of local alignment. To verify the effectiveness of the proposed algorithm in cover song identification, the beat-synchronous pitch class profile (PCP) feature is taken as test object and the optimal transposition index (OTI) is used to achieve the key invariance. According to the extracted features, the cross recurrence plot (CRP) is constructed and the similarity is computed. It is shown from the experimental results that the proposed algorithm can achieve higher identification accuracy than the traditional alignment algorithms, e. g. , dynamic time warping (DTW), cross-correlation and Qmax.