This paper aims at the task of score alignment that aligns the audio recording and its corresponding score properly. Conventional methods are mostly hard to deal with the issue: the asynchrony in the recording of simultaneous notes in the score. In this paper, we propose a note-based score alignment by means of the pitch-by-time format called piano-roll feature. One of the manners is that we develop an approach of converting audio spectrogram to piano-roll-like feature. The score-driven non-negative matrix factorization is then involved in the conversion. Secondly, the pitch-wise alignment is proposed, considering each pitch sequence (i.e., the row of pianoroll) separately. In the results, about 88% of notes match their onsets deviated from ground truth for less than 50 msbased on MIDI-Aligned Piano Sounds(MAPS) database.