Wireless Power Transfer (WPT) technology can achieve non-contact transmission of electrical energy from the power grid or batteries to electrical equipment. To solve the problem of a significant decrease in output power caused by frequency detuning in a magnetic coupled resonant WPT system, it is necessary to dynamically adjust the operating frequency of the system. The frequency tracking control tuning using phase locked loop technology is currently the most commonly used method. A new method using incomplete cross S transform (ICST) for phase difference detection is proposed in this paper. Firstly, the low-pass filter is used to eliminate the noise of the original signals, and the waveform of the original voltage signal is changed from pulsed square wave to sinusoidal wave. Then the signals output by the filter are sampled synchronously to obtain a series of discrete signal sequences, and the sampling frequency varies with the operating frequency and is determined by the PI controller. Finally, the phase vector is obtained by performing ICST on two channel discrete signal sequences, and the phase difference, which is provided for subsequent frequency tracking controller between the primary voltage and the primary current, is extracted from the phase vector. The computational complexity of S transformation is greatly reduced by utilizing incomplete S transformation. The effectiveness of the proposed method is verified by MATLAB simulation experiments. Several experiments were conducted separately. The accuracy, noise immunity, and real-time performance of this method are verified under different working conditions.