The invention discloses a slow virus carrier fluid sterile sorting method and sorting system. The sorting method comprises the following steps of S1, sterilizing a sterile isolator; S2, introducing the slow virus carrier fluid to the sterile isolator through a SART interface; S3, entering the sterile isolator, and sorting the slow virus carrier fluid filtered by a sterilization filter to a sortingbottle through a sorting tool; and S4, carrying out installing can capping on the sorting bottle by using a cap screwing tool. The sorting system comprises the sterile isolator, the sorting bottle and a feeding assembly. According to the method and the device, after the slow virus carrier fluid is introduced into the sterile isolator, the slow virus carrier fluid is sorted into the sorting bottleby using the sorting tool through sterile sorting, then the sorting bottle is sealed by using the cap screwing tool in a unified mode, the whole process is carried out in a sterile environment, the operation is simple, the pollution is not prone to generate, the production efficiency is effectively increased, and the product quality is guaranteed.