A method and a system for sterilizing a food packaging container or a food filling system, comprising a medicine sterilization process where a disinfectant aqueous solution containing a chlorine based disinfectant containing hypochlorous acid and a pH regulator is touched to the surface of the food packaging container or the line piping, apparatus of the food filling system or the surface in a room, and a heating sterilization process where surface temperature of an object is raised, wherein these processes are performed simultaneously or separately. A specified sterilization power is exhibited over a wide range of bacteria, handling is simplified, processed surface is not corroded over a long term, stench is eliminated and no special treatment of waste liquid is required.