This paper proposes a novel hybrid serial/parallel multi-frequency measurement method for measuring the impedance/inductance of eddy current sensors. Parallel multi-frequency measurement normally has a higher measurement speed, but a lower signal-to-noise ratio (SNR). In contrast, serial multi-frequency (sweeping frequency) has a lower measurement speed, but a higher SNR. The method proposed in this paper can flexibly combine these two features to deliver the desired speed and SNR according to the requirements of a specific application. A system is designed using the proposed method based on a field-programmable gate array. The composite parallel excitation signal is generated by a direct digital synthesis module, and the received multi-frequency data are simultaneously demodulated by a digital I/Q demodulator. The system is applied to measure the impedance of an inductive sensor, and a good agreement between the measurements from a commercial impedance analyzer and the designed system has been found.