Hylocereus polyrhizus cultivation started in Taiwan around the 1980s. The pulp of the fruit is edible and contains small, black, and soft seeds. The peel of the fruits are covered with bracts. The H. polyrhizus fruit is known to be rich in nutrients and minerals. To evaluate the potential applications of the agricultural wastes of H. polyrhizus, the stem, peel, and flower of H. polyrhizus were extracted with solutions of ethanol and water mixed in different ratios. Data was collected for the H. polyrhizus extract including the yield of total phenolics, the total flavonoids, and antioxidant activity, as determined by the 2-2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) radical scavenging assay. The protective effects of H. polyrhizus extract on DNA was investigated using an assay with the pUC19 plasmid. The cell proliferation and migration effects were evaluated in the NIH-3T3 fibroblast cell line. The greatest yield of extract from the stem of H. polyrhizus was 44.70 ± 1.77% which was obtained using 50% aqueous ethanol and the greatest yield of extract from the peel was 43.47% using distilled water. The stem extract, which was prepared with 95% aqueous ethanol, had the highest composition of phenolics and flavonoids as well as the best DPPH radical scavenging activity. The stem extract had excellent ABTS radical scavenging activity as well. The stem, peel, and flower extracts, which were prepared using 95% aqueous ethanol, showed excellent results in protecting themselves from DNA damage, similar to the effect of 0.3 mg/mL ferulic acid. None of the extracts were able to promote cell proliferation at concentrations of 250 μg/mL to 2,000 μg/mL in a 24 h period. The 1000 μg/mL stem and flower extracts in 95% aqueous ethanol promoted considerable cell migration after a 24 h period.