Objective To understand the infection, morphological and molecular identification of Clonorchis sinensis metacercariae in Pseudorasbora parva in multiple regions of China. Methods From August 2022 to January 2024, P. parva samples were collected from 12 sampling sites of water bodies in East, South, Central, Northwest, and Southwest China. After digesting the fish, metacercariae were isolated for morphological identification. From each sampling site, individual metacercariae in infected fishes were isolated individually to extract DNA， of which 16S rDNA was amplified with PCR and sequenced. Sequence alignment was conducted using BLAST, and a phylogenetic tree was constructed using MEGA7 and Fasttree2 with the maximum likelihood method. SD rats (n = 12) and Kunming mice (n = 10) were fed with metacercariae-positive P. parva (approximately 200 metacercariae per rat and 100 metacercariae per mouse). Eggs and adult worms from fecal samples and the bile ducts were collected, respectively, for morphological and identification at 25, 90 and 300 days post-infection. Data was analyzed by Microsoft Excel 2021 software. Fisher’s exact test was used for comparison between groups. Results Out of the 665 P. parva samples examined, 277 were positive for metacercariae, resulting in an average infection rate of 41.6%. Higher infection rates of P. parva were found in Hengzhou of Guangxi (6/6), Puyang of Henan (100%, 22/22), Yantai of Shandong (98.4%, 122/124), Fuyang of Anhui (75.0%, 24/32), Hanzhong of Shaanxi (49.2%, 95/193), and Ningde of Fujian (5/19). The isolated trematode metacercariae samples were morphologically identified as of C. sinensis. PCR amplification and sequencing results showed that the amplified about 400 bp fragment matched to the sequence of 16S rDNA of C. sinensis, revealing 100% identity (GenBank accession no.: MT607652.1). Phylogenetic analysis indicated that the isolated metacercariae clustered with C. sinensis in the same branch. At 25 and 90 days post-infection, no eggs or adults were found in mouse feces or bile ducts, while eggs were found in rat feces. At 300 days post-infection, eggs were found in the feces of two rats, and adults were isolated from the bile ducts of three rats. The eggs and adults exhibited typical morphological characteristics of C. sinensis. Conclusion The present study domonstrated that C. sinensis infection at varying degrees was found in P. parva from Hengzhou, Guangxi, Puyang, Henan, Yantai, Shandong, Fuyang, Anhui, Hanzhong, Shaanxi, and Ningde, Fujian. The 16S rDNA gene combined with the morphological characteristics can effectively identify C. sinensis metacercariae in P. parva.