High-precision magnetic field measurements are crucial for understanding Earth’s internal structure, space environment, and dynamic geomagnetic variations. Data from the Fluxgate Magnetometer (FGM) on the Macau Science Satellite-1A (MSS-1A), added to data from other space-based magnetometers, should increase significantly the ability of scientists to observe changes in Earth’s magnetic field over time and space. Additionally, the MSS-1A’s FGM is intended to help identify magnetic disturbances affecting the spacecraft itself. This report focuses on the in-flight calibration of the MSS-1 FGM. A scalar calibration, independent of geomagnetic field models, was performed to correct offsets, sensitivities, and misalignment angles of the FGM. Using seven months of data, we find that the in-flight calibration parameters show good stability. We determined Euler angles describing the rotational relationship between the FGM and the Advanced Stellar Compass (ASC) coordinate system using two approaches: calibration with the CHAOS-7 geomagnetic field model, and simultaneous estimation of Euler angles and Gaussian spherical harmonic coefficients through self-consistent modeling. The accuracy of Euler angles describing the rotation was better than 18 arcsec. The calibrated FGM data exhibit good agreement with the calibrated data of the Vector Field Magnetometer (VFM), which is the primary vector magnetometer of the satellite. These calibration efforts have significantly improved the accuracy of the FGM measurements, which are now providing reliable data for geomagnetic field studies that promise to advance our understanding of the Earth’s magnetic environment.