External administration of hydrogen gas (H2) benefits plants from multiple environmental stimuli. However, the physiological significance and molecular mechanism of H2 in ultraviolet-B (UVB) irradiation are largely unexplored. Here, the biological function of H2 in the regulation of plant UVB-tolerance was investigated by using hydrogen-rich water (HRW). Results showed that the exposure of alfalfa seedlings to UVB irradiation increased endogenous H2 production. Pretreatment with HRW mimicked the UVB-induced endogenous H2 production. Corresponding UVB-triggered toxic symptoms, in terms of lipid peroxidation and overproduction of reactive oxygen species (ROS), as well as the subsequent growth inhibition, were markedly mitigated. Metabolic profiling analysis by using ultra performance liquid chromatography-mass spectrometric (UPLC-MS), identified 40 (iso)flavonoids in UVB-treated alfalfa plants, with 22 kinds was increased by HRW. These changes resulted in the alternation of (iso)flavonoids profile, with the effective promotion of isoflavone and flavanone subfamilies in particular. These compounds included afromosin, afromosin 7-O-β-D-glucoside-malonate, daidzein, formononetin 7-O-β-D-glucoside-6''-O-malonate, garbanzol, matteucin and naringenin. In vitro tests further showed that the HRW-modulated (iso)flavonoids profile upon UVB stress possessed advanced ROS-quenching and antioxidant capacities under our experimental conditions. Meanwhile, UVB-triggered upregulation in the transcription levels of (iso)flavonoids biosynthetic-related genes were substantially strengthened by HRW. The activities and related transcripts of representative antioxidant enzymes were also induced. Taken together, our findings indicate that HRW confers tolerance to UVB-induced oxidative damage partially by the manipulation of (iso)flavonoids metabolism and antioxidant defence in Medicago sativa L.