The CSES high precision magnetometer (HPM), consisting of two fluxgate magnetometers (FGM) and one coupled dark state magnetometer (CDSM), has worked successfully for more than 5 years providing continuous magnetic field measurements since the launch of the CSES in February 2018. After rechecking almost every year’s data, it has become possible to make an improvement to the in-flight intrinsic calibration (to estimate offsets, scale values and non-orthogonality) and alignment (to estimate three Euler angles for the rotation between the orthogonalized sensor coordinates and the coordinate system of the star tracker) of the FGM. The following efforts have been made to achieve this goal: For the sensor calibration, FGM sensor temperature corrections on offsets and scale values have been taken into account to remove seasonal effects. Based on these results, Euler angles have been estimated along with global geomagnetic field modeling to improve the alignment of the FGM sensor. With this, a latitudinal effect in the east component of the originally calibrated data could be reduced. Furthermore, it has become possible to prolong the updating period of all calibration parameters from daily to 10 days, without the separation of dayside and nightside data. The new algorithms optimize routine HPM data processing efficiency and data quality.