Abiotic stress, such as drought, osmotic, and salinity stresses, seriously affects plant growth and crop production. Studying stress-resistant genes that enhance plant stress tolerance is an efficient way to facilitate the breeding of crop species with high stress tolerance. In this study, we reported that the core circadian clock component, theLATE ELONGATED HYPOCOTYL(LHY) orthologueMtLHY, plays a positive role in salt stress response inMedicago truncatula. The expression ofMtLHYwas induced by salt stress, and loss-of-function mutants ofMtLHYwere shown to be hypersensitive to salt treatment. However, overexpression ofMtLHYimproved salt stress tolerance through a higher accumulation of flavonoids. Consistently, exogenous flavonol application improved the salt stress tolerance inM. truncatula. Additionally,MtLHYwas identified as a transcriptional activator of the flavonol synthase gene,MtFLS. Our findings revealed thatMtLHYconfers plant salt stress tolerance, at least by modulating the flavonoid biosynthesis pathway, which provides insight into salt stress tolerance that links the circadian clock with flavonoid biosynthesis.