Chitin is the main component of mollusk shell organic scaffold and its metabolism is important for shell mineralization. Chitinase with the function of chitin hydrolysis plays a key role during chitin metabolism process and is related to the formation process of shell organic scaffold. In this study, by the mass spectrum analysis of shell protein, it was proved that chitinase had an abundant amount in the shell of Chlamys farreri. The cDNA sequence of gene chitinase was obtained by RACE and its full length is 1587 bp, coding 439 amino acid residues. Analysis of chitinase protein sequence with bioinformatics software shows that it has a conservative function domain existing in chitinase protein family with the function of chitin hydrolysis. Chitinase in C. farreri had a much higher expression level in the mantle tissue than in other tissues, especially the area of mantle edge. In the process of shell regeneration after shell notching, the expression level of chitinase showed a decreasing tendency indicating that chitinase responded as a negative regulatory factor during shell regeneration. After knocking down the expression of chitinase, the structure of the mineral slices was irregular and fused with a fuzzy shape and unclear boundary. In conclusion, it is suggested that chitinase in C. farreri might be related to the formation of shell organic scaffold with its function of chitin hydrolysis, which is also important during the process of shell biomineralization.