To provide a sterilization method of container-packaged food which has a high effect on mixture food of solid food/soup and a filling system where all processes and devices can be simplified, a pre-seal lid material (PS), that has been cut to a dimension covering the opening of a cup filled with solid food, e.g. a dimension corresponding to the outer circumference of the flange of the cup, is fixed to a cup holder (CH) at a position for covering the cup opening by means of a holding bolt (31a) without being fusion bonded to the cup flange portion (CF), while a ventilation state between the head space of the cup and the air in a sterilization chamber is maintained. Thereafter, steam sterilization to the cup is performed in the sterilization chamber and the cup is transported to a clean box, filled with sterilized soup.