Ferromanganese ores is an important raw material for manganese and iron beneficiation and smelting. It is difficult to separate manganese and iron efficiently due to factors such as isomorphism and fine particle embedding. The technological process of hydrogen based mineral phase transformation magnetic separation was established, and the effects of roasting temperature, roasting time, reduction gas concentration and total gas flow on the separation of ferromanganese and the conversion rate of manganese divalent were investigated. The test results show that under the conditions of roasting temperature 660°C, roasting time 30 min, CO:H2=1:3, reduction gas concentration 60%, total gas volume 500 mL/min, and magnetic field intensity 1070 Oe, the iron concentrate with iron contend of 55.24%, recovery rate 91.07%, and manganese concentrate with full manganese contend of 34.80%, recovery rate 77.11%, and conversion rate of bivalent manganese 88.79% can be obtained. The results of chemical composition analysis, XRD analysis and SEM-EDS analysis show that manganese minerals and iron minerals have been effectively separated.