A magnesium ion based organic secondary battery (MIOB) is fabricated by using polytriphenylamine as the cathode, perylene diimide–ethylene diamine as the anode and an anhydrous acetonitrile solution of magnesium perchlorate as the electrolyte. Based on a dual-ion battery mechanism, the MIOB manifests high capacities and good cycling stability. Moreover, the good electrochemical properties of the MIOB can still be reserved even at low temperatures and in flexible pouch cells. The excellent battery performance of the MIOB can be attributed to the synergistic effect of the dual-ion energy storage mechanism and the utilization of organic electrode materials.