Frequency-modulated (FM) signals are widely used in sensing, measurement, and signal detection due to their strong anti-interference and easy transmission characteristics. Although the high-precision measurement methods for static signals are quite complete, the high-precision measurement methods for dynamic FM signals still need to be studied, and the measurement accuracy in the high-sampling system still has room for improvement. Traditionally, the equal-precision measurement method is widely applied in most scenarios. However, its accuracy is limited by the quantization error of ±1 word and the sampling gate time, making it difficult to improve the frequency measurement accuracy while ensuring a high sampling rate at the same time. In this paper, a high-precision feedback frequency measurement system with the capability to eliminate the quantization error of ±1 word is proposed. The proposed system consists of two stages, the rough measurement stage based on the equal-precision measurement method and the precise measurement stage based on the negative feedback tracking architecture using the phase–frequency detector (PFD) and direct digital synthesizer (DDS). The effectiveness and feasibility of the system are verified by both simulation and experiment. At the sampling rate of 2 kHz, the frequency measurement accuracy is improved by more than 30 dB.