As one of traditional and dominant species of famous fruits in South China, Hylocereus undulates is considered as the important fruit resources, however, the constituent properties of Hylocereus undulates stems have not been known. Therefore, the molecular characteristics of extracts from Hylocereus undulates stems are studied to further utilize the resources. The result showed that there were many toxic substances in the extracts of Hylocereus undulates stems, suggesting that Hylocereus undulates stems should not be used as food. FTIR spectra showed that there were many active groups in the extracts of Hylocereus undulates stems, suggesting that Hylocereus undulates stems contain many bioactive substances. The result indicated that the extracts of H. undulates stems have huge potential resources.