The invention relates to a continuous perfusion apparatus, in particular to a tissue fragment collection and discharge liquid protection system and an operating method thereof. The tissue fragment collection and discharge liquid protection system comprises a cutting tool, wherein the cutting tool communicates with a tissue collection component; the tissue collection component communicates with a waste liquid collection component; and the waste liquid collection component communicates with a discharge liquid protection component. By virtue of the tissue fragment collection and discharge liquid protection system and the operating method thereof, service performance is further enhanced and operations are convenient.