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Background: Hydrogen gas (H2) is a newly-discovered signaling molecular that plays an important role in plants. This study investigated physiological and molecular mechanisms of hydrogen-rich water (HRW)-mediated beneficial effects on maize roots exposed to saline stress. Results: The results showed that growth of maize seedlings treated with 150 mM NaCl was greatly reduced. Under saline stress, 50% HRW diminished lipid damage in root which was confirmed by malondialdehyde (MDA) content assay and root histochemical staining, and the decreased activities of dismutase (SOD) and peroxidase (POD) further verified the reduced oxidant damage in roots cells under saline stress. HRW up-regulated the expression of ZmSOS1, ZmSKOR, and especially CDPK21 under saline stress, and it also stimulated the activities of PM H+-ATPase and tonoplast H+-ATPase and H+-PPase in maize roots. Thereby, Na+ content was decreased and K+ uptake was increased with the application of HRW. Conclusion: In summary, under saline stress, exogenous HRW application on maize roots up-regulated the key genes expression, improved H+-transport activity and thereby maintained the Na+/K+ balance, diminished oxidant damage and therefore promoted the root growth and biomass accumulation. Our results suggested exogenous HRW treatment on maize could improve root development under saline conditions and might be applied to alleviate salinity stress.