Charybdis japonica predominantly inhabits the intertidal zones and has high desiccation tolerance. We present the first chromosome-level C. japonica genome, which contains 51 chromosomes, and the revised genome is 1431.02 Mb in length and has a contig N50 size of 29.67 Mb. Among the contigs, 91.42% were anchored to 51 chromosomes. Additionally, 824.02 Mb repeat elements, 30,900 coding genes, 474 miRNAs, 15,570 tRNAs, 309 rRNAs, and 157 miRNAs were identified in the C. japonica genome. The whole-genome resequencing data can contribute to the identification of sex-related single-nucleotide polymorphisms and insertion–deletion mutations. The 0-10,120,000 bp of chromosome 37 is the sex-determining region of C. japonica. Comparative genome analysis identified 1,138 C. japonica-specific gene families. Phylogenetic analysis showed that C. japonica has a close relationship with Portunus trituberculatus, which also belonged to family Portunidae, and differentiated 42.1-135.5 million years ago. Demographic history analysis suggested that the maximum effective population size of C. japonica was maintained until 0.5×105 years ago. Relative evolution rate showed that C. japonica evolved slower than Daphnia magna, Penaeus vannamei, and P. trituberculatus. Compared with other species, metabolism rate, oxygen supply, oxidative stress, and various transporter-related genes were expanded or underwent positive selection in C. japonica, which might contribute to C. japonica’s ability to overcome diverse stresses in drought environment. Decoding the present genome provides valuable information for revealing the desiccation-adaptive and sex-determining mechanisms of C. japonica and also enriches the genetic information to explore the evolutionary history and environmental adaptation strategies of other Portunidae crabs.