Tridacna crocea are some of the most colorful members of the giant clam family, which belongs to the Bivalvia. Here, we firstly report a high-quality, chromosome-scale Tridacna crocea reference genome sequence of 1.30 Gb, with a scaffold N50 of 56.38 Mb and a contig N50 of 1.29 Mb, which was assembled by combining PacBio HiFi reads and Hi-C sequencing data. Repetitive sequences accounted for 71.60% of the assembly length, and 25,440 protein-coding genes were annotated.