This paper presents a method to estimate the coupling factor of coil-system during the operating of wireless power transfer system. In this method, the excitation signal is generated by the inverter of wireless power transfer system. The current response to the excitation signal is analyzed in frequency domain to estimate the coupling factor. In this paper, the signal model that utilized to estimate the coupling factor is first derived, which revealed the mathematical relationship between the current response to the excitation and the coupling factor. Second, based on the signal model, the estimation method is implemented and verified in the test bench. The results show that the errors of the estimated values are lower than 0.025 for the coupling factors in the range of 0.2 to 0.4 . The estimation update rate of 500 kHz is achieved. Therefore, the proposed method could be interesting for some WPT applications that need estimated coupling factor in real-time during power transfer.