The invention relates to an enzyme composition with the efficacy of strengthening kidney and tonifying Yang. The enzyme composition is prepared from the following components: 1 to 15 weight parts of probiotics, 10 to 120 weight parts of enzyme combination stoste and 10 to 80 weight parts of traditional Chinese medicinal extract; the enzyme composition is formed by treating the traditional Chinese medicinal extract by a sterilization process, then mixing the treated traditional Chinese medicinal extract with the enzyme combination stoste, inoculating a probiotic group and performing airtight fermentation. The traditional Chinese medicinal extract is prepared by extracting the following crude drugs in parts by weight: 2 to 10 parts of rhizoma dioscoreae, 2 to 10 parts of sea cucumber, 1 to 8 parts of morchella, 2 to 10 parts of rhizoma imperatae, 2 to 8 parts of chenopodium quinoa, 1 to 8 parts of root or fruit of fourpetal rose, 0.5 to 6 parts of sea horse, 0.5 to 6 parts of rhizoma curculiginis, 0.2 to 3 parts of sunflower stem pith, 0.5 to 6 parts of fructus jujubae and 0.5 to 5 parts of radix notoginseng. According to the enzyme composition, the probiotics and functional oligosaccharide are combined for use, and traditional Chinese medicinal components are added; the enzyme composition has the efficacy of strengthening kidney and tonifying Yang, and benefiting essence and tonifying Qi.