A plenty of non-coding RNAs (ncRNAs) have been identified through the application of high-throughput analysis of the transcriptome, and this has led to an intensive search for possible biological functions attributable to these transcripts. In this study, the gonad tissue of the two-year-old Crassostrea gigas of same family cultured in Rizhao Huanghai area was used to identify a large number of miRNA, lncRNA and circRNA by small RNA-seq and RNA-seq, and their biological characteristics were analyzed. The results showed that, with Danio rerio as a reference, 25-30 known miRNA matures and 51-63 known miRNA precursors was obtained, 53-71 new miRNA matures and 53-77 new miRNA precursors were predicted. The length of miRNA in C. gigas ranged from 18-26 nt, where the largest number was in the 20-22 nt and the first nucleotide position tended to be U. 2 302-2 349 known lncRNA transcripts were obtained, and 20 083-24 114 new lncRNA were predicted. Among them, the percentage of the intergenic lncRNA, intronic lncRNA and antisense lncRNA was 29.0%, 62.1%, and 8.9%, respectively. The data showed that genomic characteristics of lncRNA in C. gigas were similar to those of other eukaryotes. Compared with mRNA, the transcript and open reading frame of lncRNA were much shorter at length and much lower at expression level. 383 circRNA transcripts were obtained, of which the average percentage of 88.54% came from exon, 4.51% came from intronic and 6.95% came from intergenic. The data showed that the endogenous circRNA have a lot of miRNA target sites. This study revealed the basic biological characteristics of miRNA, lncRNA and circRNA in C. gigas. The results laid the foundation for the subsequent research on the expression rules and biological function of regulatory non-coding RNA in C. gigas.