The work aims to explore the synergistic effect of natamycin and ε-polylysine on the storage quality of pitaya to provide reference for the preservation technology of pitaya. The red-fleshed pitaya was used as the material, and the pitaya was treated with three compound concentrations (the ratio of natamycin to ε-polylysine was 1∶1 and the concentrations were 400, 800 and 1 200 mg/L, respectively, which were recorded as treatment 1, treatment 2 and treatment 3, respectively), and stored at (25±2) ℃ and (75±5%) RH. The changes of sensory indexes, contents and antioxidant enzyme activities of pitaya were analyzed. The results showed that compared with the control group, the mass loss rate of the three treatment groups was significantly reduced by 45.50%-57.06% (P<0.05), and the decay rate was significantly reduced by 16.31%-38.30%. The hardness and L value of pitaya was decreased by 8.88%-21.02% and 4.25%-6.24%, respectively. The total soluble solids (TSS) content and respiratory intensity of pitaya were decreased by 3.13%-11.79% and 2.41%-46.76%, respectively. During storage of 10 d, the content of malondialdehyde (MDA) was decreased significantly by 19.47%-33.98%. The activities of superoxide dismutase (SOD) and peroxidase (POD) were significantly increased by 1.09%-27.59% and 1.11%-32.77%, respectively. The activity of catalase (CAT) increased by 11.52%-36.19% within 8 d of storage. The activity of ascorbate catalase (APX) was significantly increased by 1.73%-23.98% at 12 d of storage. Comprehensive analysis shows that the three treatment groups can delay the increase of weight loss rate and decay rate of pitaya, slow down the decrease of peel L value and hardness, reduce respiratory intensity and MDA content, and increase SOD, CAT, POD and APX activities. Among them, treatment 1 (400 mg/L ε-PL+400 mg/L natamycin) can better maintain the commercial quality of pitaya.