The invention discloses a germinated whole grain and a preparation method thereof, and belongs to the technical field of deep processing of grains. The whole grain is subjected to ultrasonic washing, high-voltage pulsed electric field treatment, biological enzymolysis or combined high-voltage pulsed electric field and biological enzymolysis treatment in a soaking process, and a segmented soaking and germination manner for germination is adopted, so that the sensory quality, germination yield and quality of a germinated whole grain product are improved, and germination loss is reduced. The preparation method is simple, low in soaking and germination temperature, short in cycle, energy-saving and environment-friendly. The content of functional, nutritional and bioactive substances in the germinated whole grain product is remarkably increased, and food safety is remarkably improved. For example, for brown rice, germinated brown rice prepared by the preparation method has gamma-aminobutyric acid content of 303.8 to 312.6 mg / 100 g, glutathione content of 16.8 to 18.3 mg / 100 g, IP6 content of 460.8 to 484.4 mg / 100 g and dietary fiber content of 3.5 to 3.6 mg / 100 g.