Objective Panax notoginseng possesses remarkable pharmacological activities including hemostatic, blood-activating, and anti-inflammatory effects, holding significant economic value in traditional Chinese medicine and health products. This study employed high-throughput transcriptome sequencing to systematically analyze the transcriptome data of P. notoginseng leaves, aiming to identify novel viral isolates, characterize their genomic features and taxonomic classification, and detect the virus occurrence in P. notoginseng via RT-PCR. Methods P. notoginseng samples were collected from major production areas such as Wenshan, Yunnan. High-throughput transcriptome sequencing was performed using the Illumina HiSeqTM 2500 platform. Virus-specific primers were designed for RT-PCR amplification, followed by cloning and Sanger sequencing for validation. Representative RdRp amino acid sequences from GenBank were used to construct a phylogenetic tree, and the taxonomic position of the novel virus was determined based on genomic structure and sequence similarity. Results A novel dsRNA virus, tentatively named Panax cryptic virus 1(PcV1-WSPnV207), was identified in P. notoginseng. Its genome contains two non-overlapping ORFs: ORF1 encoding a capsid protein and ORF2 encoding an RNA-dependent RNA polymerase. Phylogenetic analysis clustered this virus with Deltapartitivirus species, supporting its classification as a new member of this genus. The virus was detected in multiple P. notoginseng cultivation regions (Wenshan, Shilin, and Honghe) with an overall detection rate of 55%. Conclusion PcV1-WSPnV207 represents a new species within the genus Deltapartitivirus(family Partitiviridae), exhibiting widespread distribution in major P. notoginseng production areas with a high incidence rate(55%). This study not only expands the known viral diversity in P. notoginseng but also provides new insights into the taxonomy and evolutionary relationships of Partitiviridae.