Trypsin is a novel superoxide scavenger. In this study, it was strikingly noticed that 6 significantly expressed PODs did not interact with any other antioxidant enzymes. The correlation between lignin and POD were revealed. the synergistic mechanisms of trypsin and POD plus lignin related genes (PODLs) were evaluated in Hylocereus undatus. Trypsin significantly improved the storage quality of H. undatus, including weight loss impediment, increase of lignin contents, decrease in levels of reactive oxygen species, cell permeability and membrane lipid peroxidation. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses of the transcriptome profiles of H. undatustreated with trypsin revealed that important antioxidant signal pathway, such as hydrogen peroxide catabolic process, cellular response to oxidative stress, were induced; while lignin catabolic process was impeded by trypsin.With trypsin treatment, PODLs in the pathways of “Phenylpropanoid biosynthesis”, “N-Glycan biosynthesis” and “Tyrosine metabolism” were regulated by up or down patterns. These results indicated that trypsin relieved pitaya of pressure of oxidative stress and exhibited the protection on pitaya during storage. These results indicated that trypsin relieved pitaya of pressure of oxidative stress and exhibited the protection on pitaya during storage. In addition, the results of protein-protein interaction (PPI) networks suggested that CEV1, CESA1 and OMT1 act as hubs of PODLs induced by trypsin during storage of H. undatus. Especially, through either KEGG or PPI network analysis, flavone 3'-O-methyltransferase 1 (OMT1) deeply interacted with the PODs which synergize with trypsin. The lignin biosynthesis induced by trypsin might play key roles in the mechanisms of fruit quality improving during storage ofH. undatus.