The invention discloses a natural conditioning and nourishing ferment and a manufacturing method thereof. The ferment comprises the following raw materials in parts by mass: 1-80 parts of primarily fermented liquid, 1-30 parts of probiotics, 1-30 parts of enzymes, 1-10 parts of Chinese herbal medicines, 1-30 parts of fruits, 1-30 parts of vegetables, 1-30 parts of edible mushrooms, 1-30 parts of edible algae, 1-30 parts of maltose, and 1-30 parts of honey. The primarily fermented liquid comprises the following raw materials in parts by mass: 1-50 parts of corncobs, 1-15 parts of wheat, 1-30 parts of stem rice, 1-50 parts of brown rice, 1-50 parts of rice bran, 1-50 parts of black soya beans, 1-10 parts of black glutinous rice and 1-10 parts of semen sesami nigrum. The ferment is prepared by compounding the vegetables, the fruits, the edible mushrooms, the edible algae and the traditional Chinese medicinal materials with the enzymes and fermenting by the probiotics. By adopting the ferment, the integrated conditioning properties of a plurality of plants such as fruits and vegetables and traditional Chinese medicinal materials are compounded, and the natural conditioning and nourishing ferment is free of toxic and side effects. The ferment can be used as a food, also can be added to other foods and beverage, and the natural conditioning and nourishing effects are achieved.