Improving the precision and sampling rate of the resonance frequency of cesium atoms is the key to enhancing the same factors of an airborne optically pumped cesium magnetometer (AOPCM). Aiming at the existed problems of AOPCM and characteristics of resonance signal, this paper proposes a high-precision and fast-sampling frequency measurement method based on carry chains of Field-Programmable Gate Array (FPGA). In order to achieve a fast-sampling rate, an improved equal precision frequency measurement method is proposed to measure the standard signal and the resonance signal continuously. Besides, by using the serial full adder to connect FPGA carry chains to a delay line, the delay line is used to compensate the unsynchronized clock edge, so the counting error can be reduced, and the precision of frequency measurement can be improved greatly. Experiments show that the frequency resolution is 0.014 nT and the relative error is lower than 2 × 10-6 when the sampling rate is 500 Hz. The experimental result indicates that the proposed method improves the precision and sampling rate of resonance frequency measurement greatly. Consequently, the precision and sampling rate of AOPCM can be improved.