Nano-structured iron-manganese oxides composite was prepared by annealing of natural Mn-rich limonite at different temperatures (500, 600, 700, 800°C). Their SCR performances of NO removal by NH3 were evaluated, and SEM, TEM, XRD, XRF, BET, XPS, Raman, NH3-TPD were utilized to analyze the catalytic mechanism. The results indicated that after annealing at 500°C, the as-prepared iron-manganese oxides exhibited the best SCR performance in NO conversion and N2 selectivity (over 80%) at the temperature window of 150–300°C. An increase in annealing temperature from 500 to 800°C significantly increased the particle size resulting in the decrease of surface areas, active sites, and then SCR performances. The experimental results suggested the natural Mn-rich limonite was an excellent precursor for preparing iron-manganese oxides and possessed excellent SCR performance of NO removal by NH3. This study will provide a novel way for the preparation of SCR catalyst and exploit a new application field for natural limonite.