To explore the molecular mechanisms of Ipomoea cairica invasiveness insouth China, the de novo transcriptomes from I. cairica and two related species, I. digitata and I. nil,were sequenced and assembled.There were5 6551 all-unigenes obtained by assembling the reads, among them 56522 all-unigenes were annotated, including 7815, 15615, and 180201 all-unigenes in GO, COG and KEGG databases, respectively. Moreover, the activities of NR and GS in I.cairica, keyenzyme in metabolic pathway for nitrogen, were greater than those in related species. In addition, the transcriptome data showed that the genes of key enzymes in secondary metabolism, such aspal, 4cl, cad, chs, and chi, had synergic differential expressionin I. cairica, I. digitata and I. nil. The production synthesis from metabolic pathway could play a key role in stress-resistant, growth and allelopathy of I. cairica. The RT-qPCR verification results of key genes were similar to those from transcriptome.Therefore, the result of the present research might explain partly the successful invasiveness of I. cairicain South China at the level of molecular biology.