The present invention relates to a method for making a natural fermented enzyme, and more specifically, to a method for making a natural fermented enzyme, with natural materials preserved in honey or sugar and mushrooms preserved in alcohol, which is capable of alleviating skin disease such as atopic dermatitis and the like when eaten, and removing bad smell from fishes when used as seasoning. The method for making the natural fermented enzyme of the present invention comprises: a first step of making honey preserves by preserving a first natural material in honey; a second step of making sugar preserves by preserving a second natural material in sugar; a third step of making alcohol preserves by preserving a third natural material in alcohol; a fourth step of making a natural mixture by mixing the honey preserves, sugar preserves, and alcohol preserves; and a fifth step of fermenting the natural mixture in the fourth step. The first natural material is at least one among garlic, ginger, quince, green onion roots, Metaplexis japonica fruit, Rosa multiflora fruit, balloonflower roots, Codonopsis lanceolata roots, Polygonum multiflorum, Asiasari radix roots, Asparagus cochinchinensis Merrill, Caraganae radix, dandelion, Artemisia capillaris Thunb., an elm, Acanthopanax root bark, Achyranthes japonica Nakai, Cynanchum wilfordii Hemsley, Atractylodes japonica Koidzumi, and Gastrodia elata Blume. The second natural material is at least one among Japanese apricot, grape, wild peach, mulberry, sacred fig fruit, Lysimachiae Herba, Shining-leaved gypsywort, mugwort, Aralia cordata Thunb., Angelica roots, pine needles, Saururi Herba, Chinese yam, and wild pear. The third natural material is at least one among Wolfiporia extensa (Peck) Ginns, Lentinula edodes, and Phellinus linteus.본 발명은 천연발효효소 제조방법에 관한 것으로, 보다 상세하게는 꿀 또는 설탕에 절인 천연재료와 알콜에 침지시켜 절인 버섯을 이용하여 양념으로 사용 시 생선, 어류의 잡내를 제거할 수 있으며, 섭취 시 아토피 증상 등의 피부질환을 완화시킬 수 있는 천연발효효소 제조방법에 관한 것이다.상술한 목적을 달성하기 위하여 본 발명인 천연발효효소 제조방법은 제