This paper proposes an instantaneous burst carrier frequency measurement scheme combined with timestamping counting method based on field programmable gated array. With the multiplication and phase shift of counting clock, multiple parallel counters run continuously, and the times of rising edge of measured frequency f(x) are counted simultaneously. The frequency of f(x) is calculated using the least squares line fitting method of regression analysis from the count values of f(x) and timestamping clock. Experiment results show that the proposed approach can effectively reduce the error introduced by the quantization error of ±1, improve measurement accuracy by about 2 to 3 digits, reduce measurement uncertainty by more than 20%, and diminish the processing time to 200 ns compared to traditional methods under the same measurement conditions.