With the improvement of the accuracy of the resonant sensors such as MEMS vibration beam accelerometer and vibration beam pressure sensor, the requirement of the frequency measurement accuracy is also improved. The existing frequency measurement technology usually uses the function of input capture and interrupt built in the MCU, which can not guarantee the timing constraints, and have a large gap with actual demand of measurement accuracy. In this paper, a high-precision frequency measurement scheme based on FPGA is proposed. The scheme achieves the relative frequency measurement accuracy of 1ppm under the sampling interval of 5ms, which meets the accuracy requirements of high-precision resonant sensor.