According to short wave radio signal of a certain active airborne frequency measurement instrument part device still adopts pure hardware building mode and acquisition data scattered, leading to large volume, monitoring performance is limited, the real-time problem, low accuracy and can not upgrade the system corresponding to the complex environment. A new algorithm is proposed based on the FPGA parallel processing advantages. The algorithm is in the FFT frequency estimation based on serial iterative algorithm modified for parallel computing, and the feasibility of the algorithm is verified by simulation. Hardware part, the system integrates the CPU and FPGA into a chip, greatly reduces the equipment size and development time and uses high speed 14 bit A/D 125MHz data acquisition to improve the precision of frequency measurement. Many experiments show that each module design is reasonable, the system runs stably, Compared with the original instrument of frequency measurement accuracy is improved more than 1 times, the system response time is reduced to 0.1s~0.2s, and provide effective data for real-time monitoring and fault detection of radio frequency radio signal. The measuring instrument has been successfully applied to the corresponding forces equipment examination.