Music transcription is a popular research topic recently. However, estimating pitch in polyphonic music signal encounters difficulties since the signal is a mixture of waveforms from all notes with phase differences, and estimation errors can easily arise when simple greedy methods are used. In this thesis, we propose a method to solve the problem of estimating the pitches in polyphonic music. We try to focus on separating the harmonic components of the same frequency from different notes from the observed mixtures in the music signal. With the pre-built probabilistic model of instrument timbre, which provides a reference for the reasonable ratio of each harmonic component in a pitched note, we use global optimization method to estimate optimal parameters to separate each note from the music signal. Two types of evaluation, including pitch estimation on note combinations of different intervals and pitch estimation on short music pieces, was done on the proposed system and other methods, which shows the performance and robustness of the proposed method.