When the windowed DFT algorithm is applied in harmonic measurements, the problem of initial-phase sensitivity will be encountered, this has an effect on harmonic amplitude accuracy. In this paper, the origin of initial-phase sensitivity is analyzed and the main factors that influence the level of initial-phase sensitivity are demonstrated. A method of reducing initial-phase sensitivity is proposed to increase the stability of harmonic measurements. We found that initial-phase sensitivity is determined by the side lobe peak level of the window functions when synchronous deviation is fixed. In addition, increasing the length of the time recorded can be used to remove initial-phase sensitivity. The correctness and validity of our conclusions have been confirmed through numerical results and field tests.