Hydrothermal alteration at high-temperature vents near mid-ocean ridge is thought to produce pervasive magnetization lows on basaltic ocean crust, but the detailed alteration process is insufficiently documented. Here, we performed microscopic and magnetic analyses on a large set of hydrothermal-related basaltic samples from the Southwest Indian Ridge. Fresh basalts were chloritized and brecciated during hydrothermal alteration, where titanomagnetite nanoparticle clusters hosted in interstitial glasses were dissolved in the first order, followed by large micron-scale dendritic particles. Natural remanent magnetization was reduced from 10 0 -10 1 A/m for fresh basalts to 10 −3 A/m for fully altered basalts. Hydrothermal deposits acquired a chemical remanent magnetization of 10 −2 A/m. Our results link direct magneto-mineralogical observations to geophysical interpretations, which is important in understanding seafloor hydrothermal circulation and mid-ocean ridge geodynamics.Plain Language Summary Seafloor hydrothermal vents, also known as black chimneys, produce valuable mineral resources through fluid-rock reactions beneath the seafloor-a process called hydrothermal alteration. On basaltic ocean crust, hydrothermally altered regions are generally found to be less magnetic, which provides a way to detect seafloor hydrothermal vents. To understand the cause of this phenomenon, we studied how fluid-rock reactions modify magnetic minerals on basaltic ocean crust in the Southwest Indian Ridge. We have established a detailed alteration pathway that the primary magnetic minerals were progressively replaced by nonmagnetic minerals with increasing alteration degree and the strongly magnetized nanoparticles were preferentially consumed at the very beginning of the reaction. This finding directly contributes to magnetic surveying the seafloor hydrothermal vents and establishes the value of rock magnetic proxies for quantifying the alteration degree to trace fluid-rock reactions.