Background: Powdery mildew is one of the world’s most destructive diseases of cucurbit and the major cause of losses in its production worldwide. A number of strategies have been developed and applied to discover some suitable and alternative safe methods to manage the powdery mildew disease occurrence, but little information is regarding to screen of resistant pumpkins (Cucurbita pepo L.) germplasm and explore the mechanisms of their preventing the disease occurrence at physiological, biochemical, and molecular levels. Therefore, we evaluated and determined the ability and mechanisms of two commercial pumpkin cultivars in resistance to Podosphaera xanthii infection. Results: Compared with mock-inoculated seedlings, small and sparse spots were observed on the cultivar of Sixing F1 leaves at the 13th day after inoculation with P. xanthii, whereas a large number of disease spots or a layer of white powdery mildew were observed on the surface of Jin12 F1 leaves. Increased the inoculation time (7, 9, 11 and 13 days) significantly and continuously increased the disease incidence and index of pumpkin seedlings after inoculation. The disease incidence and index of Jin12 F1 were significantly higher than the cultivar of Sixing F1. At Day 13, the disease incidence and index of Jin12 F1 were 80.0% and 72.6, whereas the cultivar of Sixing F1 was 22.3% and 17.7, respectively. The contents of H2O2, MDA, lignin and total phenolics in the leaves of Sixing F1 and Jin12 F1 were markedly accelerated after inoculation with P. xanthii. However, the cultivar of Sixing F1 exhibited less reactive oxygen species (ROS) accumulation, a lower rate of lipid peroxidation and higher level of lignin and total phenolics contents after inoculation, whereas the cultivar of Jin12 F1 exhibited higher level of ROS accumulation and rates of lipid peroxidation, and lower level of lignin and total phenolics contents. Higher activity and transcript level of antioxidant enzymes and gene of PAL expression were observed on different tissues of both cultivars after inoculated with P. xanthii. Compared with pumpkin seedlings that were inoculated with sterile water but not P. xanthii, the level of PAL activity and gene expression in leaves, petioles and stems of Sixing F1 and Jin12 F1 were upregulated and increased significantly at different time points after inoculation. The enhancement expression of PAL activity and gene in different tissues of Sixing F1 was significantly higher than Jin12 F1, and higher in leaves, lower in petioles and stems. Conclusions: Our results indicate that the cultivar of Sixing F1 exhibited the highest ability in resistance to P. xanthii infection in comparison to Jin12 F1, and one novel possible mechanism is related to the cultivars in resistance to P. xanthii infection by activating and enhancing the antioxidative defense system and gene expression to prevent the pathogens infection.