There is a problem of harmonic phasor estimation under out-of-band interference, frequency deviation and other dynamic situations in power systems. Thus a harmonic phasor estimator based on a cosine flat-top window is proposed. First, the window coefficients of the flat-top window are obtained by the ideal amplitude response and the least squares method based on the cosine window frequency domain expression. To obtain a frequency response with zero gain at the nominal harmonic frequency, the obtained window function is combined with the frequency domain sampling theorem. Based on this, a bank of finite impulse response filters is designed by the least squares method, and they are used to estimate the harmonic phasor. Then, the frequency response of the cosine flat-top window and the harmonic phasor measurement filter is analyzed. Finally, the performance of the proposed harmonic phasor estimator is verified by different signal models under steady-state and dynamic conditions. The simulation results show that, compared with the two harmonic phasor estimators based on the Sinc interpolation function and the frequency domain sampling theorem, the proposed method has a stronger ability to suppress out-of-band interference, and more accurate harmonic phasor estimation can be realized under the various conditions. This work is supported by the National Natural Science Foundation of China (No. 51477173).