High-temperature stress severely limits the cultivation and ornamental quality of herbaceous peony, especially in low-latitude regions. The objective of this study was to reveal the potential mechanism involved in regulation of jasmonates on herbaceous peony heat tolerance through crosstalk between phytohormones and the reactive oxygen species (ROS) scavenging system. The study found that exogenous methyl jasmonate (MeJA) significantly improved thermotolerance of the low-latitude cultivar ‘Hang Baishao’ by enhancing antioxidase activities and modulating endogenous phytohormone levels. The MeJA-treated group exhibited markedly higher ratios of MeJA to zeatin riboside (ZR), gibberellic acid (GA₃), brassinolide (BR), and indole-3-acetic acid (IAA) compared with the control group; catalase (CAT) and superoxide dismutase (SOD) activities were significantly elevated relative to hydrogen peroxide (H₂O₂) content, with both ratios peaking at 36 h post-heat treatment. Transcriptomic results revealed that MeJA reshaped the expression of genes involved in jasmonic acid (JA) signaling and ROS scavenging, such as FAD4, MED25, and JAZ2 and CSD2/3, FSD1, and CAT3. Four modules including the hub genes CIPK5/6, WRKY19/40 and CYPs were identified from the weighted gene co-expression network analysis (WGCNA), which may be key players in coordinating JA signaling and antioxidant defense. This study demonstrates that MeJA enhanced herbaceous peony thermotolerance by orchestrating a regulatory network involving phytohormonal crosstalk and activation of the ROS scavenging system, and offers candidate genes for future exploration of function and interactions.