The invention discloses natural skin activating essence and a preparation method thereof. The natural skin activating essence is characterized by being prepared from the following raw materials in parts by weight: a component A: 10 to 15 parts of a seaweed extracting solution, 2 to 3 parts of allantoin, 6 to 8 parts of glycerinum, 1.2 to 1.5 parts of xanthan gum and 50 parts of deionized water; a component B: 8 to 10 parts of a Nuphar pumilum (Hoffm.) DC. extracting solution, 2 to 3 parts of glyceryl stearate, 1.2 to 1.4 parts of methylparaben, 0.6 to 0.8 part of carbomer 941, 2 to 4 parts of polydimethylsiloxane, 0.5 to 0.7 part of panthenol, 0.08 to 0.1 part of essential oil and 0.06 to 0.08 part of ethylene diamine tetraacetic acid; and a component C: 8 to 10 parts of a water nymph extracting solution, 3 to 5 parts of hyaluronic acid, 1 to 2 parts of squalane, 0.5 to 0.7 part of nicotinamide and 0.1 to 0.3 part of a preservative. Active components in a water-based plant have the effects of delaying senescence and maintaining moisture; the seaweed extracting solution can suppress peroxidation of skin lipid and delay skin senescence; the Nuphar pumilum (Hoffm.) DC. extracting solution has a good effect of suppressing tyrosinase and can inhibit formation of melanin; and the water nymph extracting solution and the nicotinamide work cooperatively and have a deep water locking effect and a good moisture maintaining effect.