Endplate chondrocyte apoptosis is an important contributor to the pathogenesis of cartilaginous endplate (CEP) degeneration that leads to the initiation and development of intervertebral disc degeneration (IDD). In this study, we hypothesized that Parkin-mediated mitophagy and nuclear factor E2-related factor 2 (Nrf2)-mediated antioxidant system played an important role in endplate chondrocyte survival under pathological conditions. Human endplate chondrocytes were stimulated with H2O2 to mimic pathological conditions. Western blotting, immunofluorescence staining, and flow cytometry were applied to detect the indicators related to mitochondrial dynamics, mitophagy, Nrf2 signaling, and apoptosis. The puncture-induced rat models were established to evaluate the changes in vivo. Our results showed that H2O2 induced oxidative stress, mitochondrial dysfunction, and apoptosis in endplate chondrocytes. These H2O2-induced detrimental effects were inhibited by pretreatment with the mitochondria-targeted antioxidant Mito-TEMPO. In addition, mitochondrial dynamics, Parkin-mediated elimination of dysfunctional mitochondria, and Nrf2-mediated antioxidant system were promoted by H2O2. Knockdown of Parkin or Nrf2 increased H2O2-induced detrimental effects. Moreover, upregulation of Parkin and Nrf2 by polydatin protected endplate chondrocytes against H2O2-induced mitochondrial dysfunction, oxidative stress, and apoptosis. Finally, puncture-induced rat models showed that polydatin exerted a protective effect on CEP and disc degeneration. Targeting Parkin and Nrf2 to improve mitochondrial homeostasis, redox balance and endplate chondrocyte survival may represent a potential therapeutic strategy for preventing IDD. Display omitted •Mitophagy and mitochondrial dynamics are promoted in H2O2-treated endplate chondrocytes.•Nrf2 signaling is activated in H2O2-treated endplate chondrocytes.•Parkin or Nrf2 deficiency enhances H2O2-induced damage to endplate chondrocytes.•Upregulation of Parkin and Nrf2 by polydatin protects endplate chondrocytes against the oxidative damage.