With high requirement setting for hard disk substrate surface quality, abrasive-free polishing (AFP) has attracted more researchers’ attention. In this paper, the influence of Mn (Ⅱ) ion on AFP of hard disk substrate in the H2O2based slurry was investigated. The experiments results show that Mn (Ⅱ) ion can effectively increase the material remove rate (MRR) and improve the planarization of hard disk substrate. Furthermore, the acting mechanism of Mn (Ⅱ) ion in AFP of hard disk substrate was analyzed. The electron spin-resonance spectroscopy (EPR) analysis shows that Mn (Ⅱ) ion in the H2O2based slurry not only can increase the concentration of ·OH free radical, but also can make H2O2decompose to ·O2–free radical. These free radicals can accelerate the chemical etching and increase the MRR of hard disk substrate.