Lysophosphaticly lcholine acyltransferase 1 (LPCAT1) is an important lipid metabolic enzyme. In order to clarify the function of HcLPCAT1 gene in carotenoid metabolism and the correlation of HcLPCAT1 gene with the shell nacre color in Hyriopsis cumingii. The cDNA full-length sequence of HcLPCAT1 gene in H. cumingii was cloned by RACE. Quantitative real-time PCR (qRT-PCR) and in situ hybridization (ISH) were used to analyze the expression pattern of HcLPCAT1 in different tissues. The effect of HcLPCAT1 on carotenoid metabolism was determined by supplementary feeding experiment. The direct sequencing method was used to screen the SNP sites related to inner shell color in the HcLPCAT1 gene. The results showed that the full-length cDNA of HcLPCAT1 was 1675bp with a 1296bp-long open reading frame (ORF) encoding 431 amino acids. HcLPCAT1 was expressed in the white and purple mussel tissues, with the expression levels being higher in the purple mussel than in the white mussel, and there was significant difference (P＜0.05) between hepatopancreas and fringe mantle. The situ hybridization analysis showed that the positive signal of HcLPCAT1 located at the outer fold of mantle, dorsal mantle, ventral mantle, the joint of outer fold and middle fold of mantle and part of middle fold. After supplementation with β-carotene to purple mussel, the expression of HcLPCAT1 gene in hepatopancreas, middle mantle and fringe mantle increased significantly (P＜0.01), and total carotenoids content (TCC) in these tissues also increased significantly (P＜0.01). The genotypes of five SNP sites on the HcLPCAT1 gene were identified to be significantly correlated with the inner shell color parameters of H. cumingii. Haplotype analysis revealed that the H1 and H3 were the dominant haplotypes in the purple mussel, and the H3, H5 and H6 were the dominant haplotypes in the white mussel. The HcLPCAT1 gene identified in this study provides a molecular basis for analyzing the carotenoid metabolism and shell color formation of H. cumingii. The selected SNPs and haplotypes of HcLPCAT1 gene related to inner shell color can be used in molecular assisted breeding.