This paper considers a melody extraction algorithm using a harmonic structure model and analyzes an effect of window length on the melody extraction. The algorithm estimates a melody pitch of each frame based on the melody definition that melody is a dominant single pitch sequence of a polyphonic audio. The algorithm performs short time Fourier transform (STFT) to find the dominant pitch sequence. However, the length of window for the STFT affects the melody extraction result because time-frequency resolution depends on the window length. Therefore, the relation between the window length for STFT and melody extraction is analyzed.