Mechanochemical method has applied to the green preparation of iron-molybdenum catalyst efficiently, and their catalytic performance was evaluated by the oxidation of methanol to formaldehyde. In order to investigate the formation process of iron-molybdenum catalyst based on mechanochemical method, various characterization techniques have been employed. Results indicate that iron-molybdenum catalyst could not be generated during ball milling process without calcining, and calcination is crucial step to regulate the ratio of MoO3 and Fe2(MoO4)3. For the formation of MoO3 and Fe2(MoO4)3 phase, 180 °C could be the key turning temperature point. Fe2(MoO4)3 and MoO3 phases are concurrently emerged when Mo/Fe atomic ratio exceeds 1.5. The aggregation of Fe2(MoO4)3 is severe with the increasing calcination temperature. Fe2(MoO4)3 is stable below 600 °C, while MoO3 phase could be subliming with the increasing temperature. The catalytic performance of iron-molybdenum catalyst has closely correlation with the phase compositions, which can be controlled by synthesis temperature and Mo/Fe molar ratio. The iron-molybdenum catalyst with Mo/Fe atomic ratio of 2.6 calcined at 500 °C for 4 h showed the best methanol conversion (100%) and formaldehyde yield (92.27%).