The invention belongs to the technical field of selenium-rich wine preparation, and discloses a biological organic selenium-rich functional active walnut wine and a preparation method thereof. The wine is prepared from peeled semen juglandis and a medicinal and edible dual-purpose traditional Chinese medicine formula, wherein the medicinal and edible dual-purpose traditional Chinese medicine is prepared from one or more than two kinds of lycium chinensis, herba epimedii, herba cistanche, semen hoveniae, radix astragali, cynomorium songaricum, radix morindae officinalis, radix glycyrrhizae, radix puerariae, semen hoveniae, rhizoma polygonati and cortex eucommiae, wherein one part of medicinal and edible dual-purpose traditional Chinese medicine is soaked in 50-100 parts of grain liquor, wherein the wine is 50 degrees, and brewing is carried out by small-molecule purified water or micro-molecule purified water. The selenium-rich functional active walnut wine comprises 0.24-0.5mg/kg of total selenium content and 0.2-0.5mg/kg of organic selenium, wherein the content of active ingredients is clear, the color is transparent, the natural grain wine is mellow, the taste is soft and sweet,and the wine has the effects of safely supplementing selenium, preventing and treating selenium deficiency diseases, nourishing yin and strengthening yang, and provides guarantee for the quality of aseries of biological selenium-rich functional active walnut wine.