Ipomoea pes-caprae (L.) R. Brown is one of the perennial wild species of sweetpotato, a perennial vine plant which grows on tropical and subtropical beaches. It is one of the landscaping plants in coastal areas with strong salt tolerance. The study of Ipomoea pes-caprae genome-wide can provide reference for the improvement of salt-tolerant varieties of Sweetpotato and the innovation of salt-tolerant sweet potato germplasm resources. In order to reduce the blindness of whole-genome deep sequencing, this experiment aims to understand the genome overview and provide insight for the following mapping of the whole genome. We performed the experiments in preliminary estimation of the genome size of Ipomoea pes-caprae by flow cytometry, generation of high-throughput sequencing datasets, and the bioinformatics analysis of genomic profiles such as Ipomoea pes-caprae GC content, heterozygosity, and repeat sequences. The results showed that the genomic size by using the flow cytometry was 1012.99 Mb, and the clean data of Ipomoea pes-caprae was 21.71 Gb by genome-wide Survey. By integrated analysis with 30x genomic dataset, its genome size was re-estimated to be 1041.65 Mb. K-mer analysis suggested 74.52% of repeated sequences of the Ipomoea pes-caprae genome. The heterozygosity rate was 0.99%. The initial depth of GC and the content distribution were abnormal after initial assembly. The stratification phenomenon may be related to the high heterozygous rate of the Ipomoea pes-caprae genome. Thus, this work reported the preliminary information of the Ipomoea pes-caprae genome, which lays a foundation for further genome-wide deep sequencing and salt tolerance gene mining.