In this study, a feasible strategy, named hydrogen mineral phase transformation (HMPT) technology, is proposed and employed to achieve efficient and clean recovery of Hainan Shilu refractory iron ore (HSRIO). The influences of HMPT roasting temperature, roasting time, and H2 concentration on the separation index of HSRIO are investigated. Under the optimal experimental conditions, the iron concentrate grade increases from 62.5% to 67.9%, and the iron recovery increases from 65.0% to 94.7% compared with the original beneficiation process. In addition, the evolution of mineral phases, magnetic properties, and mineral microstructures is analyzed using XRD, VSM, SEM, and high-temperature hot-stage microscopy. It is revealed that the transformation of hematite to magnetite occurs during the HMPT process, with the newly formed magnetite exhibiting a loose and porous reticulation structure. This study is of guiding significance for the development of Hainan Shilu refractory iron ore with high efficiency and zero-carbon emission.