The parasitic disease scuticociliatosis poses significant economic losses to shrimp culture. In this study, an unidentified species of ciliates was discovered in Litopenaeus vannamei. Morphological and molecular analyses were conducted to identify the parasite species, while a reinfection experiment was performed to assess its virulence towards L. vannamei. Simultaneously, Chinese herbal medicine was assessed for potential prevention and control of this pathogen. The results revealed that the SSU rDNA (93.87%), LSU rDNA (98.20%), and ITS1-5.8S-ITS2 rDNA (87.10%) genes exhibited high homology with Metanophrys sinensis, suggesting its classification within the genus Metanophry sp. The reinfection experiment demonstrated median lethal dosages of 6638 individuals/mL at 24 h and 4658 individuals/mL at 48 h for this ciliate on the host L.vannamei. In terms of drug control, we conducted a screening of 23 Chinese herbal extracts through in vivo injection trials and observed that Mume fructus extract exhibits potent biocidal activity. Specifically, the M. fructus extract solution with a final concentration of 5 mg/mL (0.5% v/v) eliminated all ciliates within 3 h. In conclusion, this study identified the ciliate parasite as Metanophrys sinensis and demonstrated its virulence to Litopenaeus vannamei. Mume fructus extract was found to effectively control the parasite, offering potential for managing scuticociliatosis in shrimp culture.