Social development is possible with agriculture. With the impact of environmental pollution, natural disasters, climate change, food security, and population growth, interdisciplinary "new agriculture" is becoming an important trend of modern agriculture. Hydrogen (H2) is the most common element on earth, making up more than 75% of the mass of the universe. Hydrogen gas is colorless, odorless, and tasteless and is considered a physiologically inert molecule and a potential source for clean energy in the future. Hydrogenated agriculture including mainly hydrogen-rich water (HRW) focuses on the molecular mechanisms underlying improved agricultural product quality. Studies have shown that H2 does not only affect plant growth and development but also affects the nutritional quality and shelf life of the fruit. Hydrogenated agriculture emerges as a promising technology for the sustainability of agricultural products in modern agricultural practices thanks to the different beneficial effects of H2 such as safety, nutritional and antioxidative properties, and high product productivity. In this review, the roles of H2 in plants, seed germination, seedling growth, root development, stomatal opening and closing, pre-harvest freshness, post-harvest freshness, and the changes caused by hydrogenated agriculture at various stages of the plant such as anthocyanin synthesis have been investigated.