Protostane triterpenes in Alisma orientale (Sam.) Juz. have unique structural features with distinct pharmacological activities. Previously we have demonstrated that protostane triterpene biosynthesis could be regulated by methyl jasmonate (MeJA) induction in A. orientale. Here, proteomic investigation reveals the MeJA mediated regulation of protostane triterpene biosynthesis. In our study, 281 differentially abundant proteins were identified from MeJA-treated compared to control groups, while they were mainly associated with triterpene biosynthesis, α-linolenic acid metabolism, carbohydrate metabolism and response to stress/defense. Key enzymes 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), squalene epoxidase (SE), oxidosqualene cyclase (OSC) and cytochrome P450s which potentially involved in protostane triterpene biosynthesis were significantly enriched in MeJA-treated group. Basic Helix-loop-helix (bHLH), MYB, and GRAS transcription factors were enhanced after MeJA treatment, and they also improved the expressions of key enzymes in Mevalonate pathway and protostane triterpene. Then, MeJA also could increase the expression of α-galactosidase (α-GAL), thereby promoting carbohydrate decomposition, and providing energy and carbon skeletons for protostane triterpene precursor biosynthesis. As well, exogenous MeJA treatment upregulated 13-lipoxygenase (13-LOX), allene oxide synthase (AOS) and allene oxide cyclase (AOC) involved in α-linolenic acid metabolism, leading to the accumulation of endogenous MeJA and activation of the protostane triterpene biosynthesis transduction. Finally, MeJA upregulated stress/defence-related proteins, as to enhance the defence responses activity of plants. These results were further verified by quantitative real-time PCR analysis of 19 selected genes and content analysis of protostane triterpene. The results provide some new insights into the role of MeJA in protostane triterpene biosynthesis