Chilling injury (CI) is a bottleneck factor constraining the refrigeration and cold chain logistics of mango fruit. Methyl jasmonate (MeJA) is an important phytohormone that can regulate multiple abiotic stresses. This study evaluated the potential effects of MeJA on CI in ‘Guifei’ mango fruit stored at 4 °C and its underlying mechanisms involved in the regulation of antioxidation and energy status. The application of 50 µM MeJA mitigated CI symptoms and improved ripening-related quality during refrigeration, as indicated by a lowered CI index, retarded declines in chlorophyll fluorescence (Fv/Fm) and chromaticity L* and advanced color transformation (from green to yellow), softening and accumulation of soluble solids. MeJA treatment repressed the increases in relative conductivity (RC), malondialdehyde (MDA) content and reactive oxygen species (ROS) (O2-. and H2O2). Reduced ROS generation in MeJA-treated fruit was a consequence of the enhancement of antioxidant enzyme activities, including superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR). Ultrastructural observation revealed that MeJA treatment protected mitochondrial structure. MeJA treatment promoted intracellular energy synthesis and utilization, as indicated by increments in intracellular adenosine triphosphate (iATP) level, activities of isocitrate dehydrogenase (IDH), α-ketoglutarate dehydrogenase (α-KGDH), succinate dehydrogenase (SDH), cytochrome C oxidase (CCO), H+-ATPase and Ca2+-ATPase as well as contents of reduced coenzymes (NADH and FADH2). In addition, the expression levels of genes (MiAPYs, MiENTs, MiPUPs and MiAPRTs) related to extracellular ATP (eATP) hydrolysis, eATP transport and iATP regeneration were upregulated in response to MeJA, contributing to maintenance of eATP/iATP homeostasis. These findings suggest that MeJA could reinforce cold tolerance in mango fruit by inhibiting oxidative stress and promoting energy metabolism. •Methyl jasmonate (MeJA) relieved chilling injury in mango fruit during cold storage.•MeJA increased the activities of antioxidant enzymes in mango fruit.•MeJA protected mitochondrial structure and promoted energy synthesis in mango fruit.•MeJA enhanced activities of mitochondrial H+-ATPase and Ca2+-ATPase in mango fruit.•MeJA maintained eATP/iATP homeostasis by regulating iATP salvage pathways.