Ipomoea cairica is a perennial creeper that has been widely introduced as a garden ornamental across tropical, subtropical and temperate regions. Because it grows extremely fast and spreads easily, it has been listed as an invasive species in many countries. Here, we constructed the chromosome-level reference genome of Ipomoea cairica by PacBio HiFi and Hi-C sequencing, with assembly size of 733.0 Mb, contig N50 of 43.8 Mb and scaffold N50 of 45.7 Mb, and BUSCO complete rate of 98.0%. Hi-C scaffolding assigned 97.9% of the contigs to 15 pseudo-chromosomes. Telomeric repeat analysis reveals that 7 of the 15 pseudo-chromosomes are gapless and telomere-to-telomere. The transposable element content of I. cairica is 73.4%, obviously higher than that of other Ipomoea species. A total of 38,115 protein-coding genes were predicted, with the BUSCO complete rate of 98.5%, comparable to that of the genome assembly, and 92.6% of genes were functional annotated. In addition, we identified 3,039 tRNA genes and 2,403 rRNA genes in the assembled genome. Phylogenetic analysis showed that I. cairica formed a clade with I. aquatica, and they diverged from each other 8.1 million years ago. Through comparative genome analysis, we reconfirmed that a whole genome triplication event occurred specific to Convolvulaceae family and in the ancestor of the genus Ipomoea and Cuscuta. This high-quality reference genome of I. cairica will greatly facilitate the studies on the molecular mechanisms of its rapid growth and invasiveness.