Rice bean (Vigna umbellata) is consumed as a common vegetable in Southeast Asia. Methyl jasmonate (MeJA) functions as an endogenous/exogenous stress signal to elicit the production of specific metabolites during sprouting. To elucidate the changes in metabolites and the effects of MeJA on rice bean sprouting, non-targeted ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry along with principal component analysis and supervised orthogonal projection to latent structure-discriminant analysis was performed to analyze the dissimilar profiles among the sprouts at different stages. Analysis of the abundance of biomarkers, such as sugars, free fatty acids, amino acids, flavonoids, benzoic acid derivatives, triglycerides, and lipids, showed the main effects of MeJA involved in the significant metabolite pathways. Our study elucidated the changes in rice bean composition and metabolites associated with various stages of sprouting and the roles of MeJA in sprout physiology. Our results can help improve this economically important grain crop.