Magnetic modulation methods especially Micro-Electro-Mechanical System (MEMS) modulation can improve the sensitivity of magnetoresistive (MR) sensors dramatically, and pT level detection of Direct Current (DC) magnetic field can be realized. While in a Low Frequency Alternate Current (LFAC) magnetic field measurement situation, frequency measurement is limited by a serious spectrum aliasing problem caused by the remanence in sensors and geomagnetic field, leading to target information loss because frequency indicates the magnetic target characteristics. In this paper, a compensation field produced with integrated coils is applied to the MR sensor to remove DC magnetic field distortion, and a LFAC magnetic field frequency estimation algorithm is proposed based on a search of the database, which is derived from the numerical model revealing the relationship of the LFAC frequency and determination factor [defined by the ratio of Discrete Fourier Transform (DFT) coefficients]. In this algorithm, an inverse modulation of sensor signals is performed to detect jumping-off point of LFAC in the time domain; this step is exploited to determine sampling points to be processed. A determination factor is calculated and taken into database to figure out frequency with a binary search algorithm. Experimental results demonstrate that the frequency measurement resolution of the LFAC magnetic field is improved from 12.2 Hz to 0.8 Hz by the presented method, which, within the signal band of a magnetic anomaly (0.04-2 Hz), indicates that the proposed method may expand the applications of magnetoresistive (MR) sensors to human healthcare and magnetic anomaly detection (MAD).