Vortex flowmeter is a fluid vibration flow meter, which is easily affected by pipeline vibration and flow field disturbance. The measurement error is large under the condition of small flow rate, especially under the interference of strong vibration, vortex signal is submerged, and it cannot be accurately measured. In this paper, a vortex flowmeter system which is resistant to strong periodic vibration is developed. Differential charge amplifier with negative voltage feedback is used to improve the ability of discharge flow signals. A frequency variance algorithm based on frequency shift strategy is proposed to reduce the influence of strong periodic vibration. Firstly, the influence of similar frequencies is reduced by frequency shift strategy. Then, according to the frequency band width of traffic signal and periodic vibration interference, the frequency of traffic signal is determined by calculating and comparing the frequency variance. The signal processing system of vortex flowmeter is developed and tested. The results show that the developed system extends the lower limit of range and can accurately extract signals under the condition of strong periodic vibration interference, and the accuracy is improved by one order of magnitude.