Abstract: The non-self-oscillating optically pumped helium magnetometer is widely used in the field of geophysical exploration. The filter, as a key module for the digitization of domestic magnetometers, plays a significant role in improving the performance of the magnetometer. In view of the limits of the current filter design, this study developed and implemented a multi-stage filter design characterized by a simple structure, low FPGA resource consumption, and user-friendly operation. Specifically, the multi-stage cascaded integrator comb (CIC) filter was cascaded with the infinite impulse response (IIR) filter, which was then embedded into a lock-in amplifier, thereby enabling signal extraction and detection. Through MATLAB simulation and FPGA implementation, the performance of this newly designed filter was verified, which can realize the extraction of the first and second harmonic signals during magnetic surveys. Furthermore, an optically pumped helium magnetometer configured with such a filter exhibited a picotesla (pT) sensitivity, satisfying the requirements of the Criterion of Aeromagnetic Survey. This new design provides technical support for the miniaturization of new-generation aerial magnetometers.