Sweetpotato is an important crop, and it boasts numerous wild relatives that possess abundant genetic variations In this study, a comparative genomic analysis was conducted using two publicly available high-quality genome of sweetpotato wild relatives. A total of 1798184 single nucleotide polymorphisms (SNPs) covering the whole genome were excavated. In additions, 2076 translocations and 84 inversions were detected. The inversions encompassed 2106 genes. Enrichment analysis showed that these genes are mainly enriched in pathways such as the biosynthesis of secondary metabolites. Among them, the breakpoints of 34 inversions are located inside the genes and may affect the structure of the genes. There are 10226 insertion-type and 11411 deletion-type structural variations (SVs) between the two genomes. We annotated these SVs and conducted gene enrichment analysis on those SVs that may affect gene function or expression. The results showed that these potentially affected genes were mainly enriched in pathways of secondary metabolites. Genes related to functions such as DNA repair and replication were enriched. Through the statistics of the synonymous substitution rate (Ks) and fourfold degenerate synonymous site (4DTv) of collinear gene pairs of two wild species and other related species, it was indicated that the common ancestor of the genus Ipomoea differentiated into different species after a whole-genome triplication event. The above research will provide strong support for the excavation of excellent variations in wild relatives of sweetpotato as well as forspecies differentiation.