Abstract: We designed and made a kind of microcontrollers frequency meter for borehole geomagnetic absolute observation by helium optically pumped magnetometer, which is suitable for the narrow space, high measurement accuracy, an easy access to upload data and automatic measurement. This frequency meter is based on ARM Cortex-M3 microcontroller, using timers’ external clock mode to count and calculate the frequency result in the interrupt service function. After many experiments, in order to further improve the measurement accuracy, the 32 MHz active temperature-compensated crystal oscillator is used to provide the main frequency signal for the chip, which improves the main frequency accuracy and reduces the code’s resource occupation rate of the CPU. The results show that the frequency meter has enough high precision that can meet the project requirements. The system error is stable, and the systemerror is 1 Hz in the range of 840.70 kHz to 1.96 MHz. Considering the specific reason for this error, we can easily compensate it by software codes and then realize a high-precision measurement.