Owing to the high resolution of magnetic force microscopes (MFMs) operating at low temperatures and high-applied magnetic fields, they can be employed to study various phenomena observed in topological magnetic materials and superconductors. In this study, we constructed a low-temperature MFM equipped with a 2–2–9-T vector magnet and a three-axis fiber-optic alignment system. The three-axis alignment device enables in situ calibration of the scanner at low temperatures as well as optimizes the intensity and sensitivity of the interferometer signal. A massive homebuilt vibration isolation table lowers the resonance frequency of the system and minimizes mechanical noise. Consequently, the minimum detectable force gradient of our proposed model is close to the thermodynamic limit of the cantilever. To demonstrate the low-temperature capability of the MFM, we obtained magnetic domain images of the van der Waals ferromagnet Fe4GeTe2 and the Abrikosov superconducting vortices of an Nb film. Furthermore, we performed field angle-dependent MFM experiments in a van der Waals magnetic insulator Cr2Ge2Te6 to verify its vector-field functionality and observed a transition in the domains from the stripe to the bubble phase with respect to the magnetic field angle. The vector-field capability of our MFM can be useful for investigating various anisotropic magnetic phenomena in topological magnetic and superconducting materials.