As a non-thermal processing technology, pulsed light is efficient, safe and environmentally friendly, and can maintain the nutrition and flavor of food to a large extent. The work aims to explore the effect of pulsed light in sterilization of low-temperature yogurt filling equipment. The sterilization effect of the pulsed light on the Aspergillus niger at different positions of different packaging containers in the low-temperature yogurt filling equipment was studied. The results demonstrated that the sterilization effect of pulsed light on Aspergillus niger increased significantly with the increase of illuminance dose. The same dose of pulsed light had significant difference in sterilizing different forms of packages, but the Aspergillus niger on the plastic bottle package was difficult to inactivate. The sterilization effects for different positions on the packaging container were different significantly. The bottom and the inner of the cover film in plastic cup package, the side and bottom of the cap, and the inner and outer of the bottle mouth in plastic bottle package,showed satisfied sterilization effect, but the threads of the cap had poor sterilization effect. In the actual production, the bacteria on the threads were difficult to inactivate, which were dead spots for sterilization and had certain risks. Compared with ultraviolet sterilization, pulsed light shows better sterilization performance and strong penetrating ability, thus it will have a broad prospect in filling equipment.