Methyl jasmonate (MeJA) is widely involved in the life processes of plants, especially playing an active role in regulating the synthesis and accumulation of metabolites. Prickly ash (Zanthoxylum bungeanum), as a species of spice tree, is rich in flavonoids throughout its entire plant, showing enormous potential for development into functional foods. Flavonoids play crucial roles in signal transduction and defense mechanisms between plants and their environment, influencing the ecological adaptability of plants. Analyzing the regulatory relationship between methyl jasmonate and flavonoid metabolites will help understand the self-protection mechanism of Zanthoxylum bungeanum under adverse stress. Research results show that the upstream promoter of CHSs (Chalcone synthase), a key gene for flavonoid synthesis, contains multiple methyl jasmonate response elements. Exogenous MeJA induction experiments proved that MeJA can significantly increase the expression levels of ZbCHS71, ZbCHS43 and ZbCHS26 in different tissues of Zanthoxylum bungeanum and directly promote the synthesis and accumulation of flavonoid metabolites. The research results help analyze the regulatory relationship between methyl jasmonate and flavonoids, and provide a reference for research on the accumulation of protective substances under stress conditions in Zanthoxylum bungeanum.