This paper studies pronunciation scoring algorithm in CALL system aiming at teaching native Chinese learn standard Mandarin. Most of the pronunciation scoring algorithms focus on non-native environment, which may not be suitable for native speakers. We bring up a new algorithm based on traditional posterior log-likelihood algorithm by weighting the initial part of Mandarin syllables, where final-initial’s duration ratio is introduced to control the weight. Experiments show that the proposed algorithm is much more effective than traditional posterior log-likelihood algorithm in the Mandarin learning system. The correlation with human score achieves an increase of 11%.