Abstract: In order to work out a viral metagenomic research method of oyster (Crassostrea spp.), we applied differential centrifugation and ultracentrifugation with sucrose gradient to obtain the virus-like particle in crude extract. After further nuclease treatment of host nucleic acid, reverse transcription and double-stranded amplification, we used Hiseq2500 platform to produce a viral genome dataset from the sample. Results show that a total of 1 661 809 000 nucleotides, including 6 647 236 reads information were obtained and further overlapped into 50 842 contigs whose total sequence length reached 14 239 389 bp. Besides, we observed good quality of reads by the control chart and so on. We scanned the GenBank virus database with data, which indicates that the known virus sequences belonged to two families (Picornaviridae, Herpesviridae) and three virus genus (Simplexvirus, Cardiovirus, Enterovirus).