The invention discloses a high-content natural shikimic acid extract product separated and prepared from waste water generated in a ginkgo leaf extract product production process and a preparing method thereof. The content of shikimic acid is higher than 98%. The waste water generated in the ginkgo leaf extract product production process is adopted as a raw material of the method, and the method includes directly subjecting the waste water to adsorption separation with anion exchange resin, allowing the eluate obtained to pass through cation exchange resin to remove sodium, subjecting a solution after sodium removal to three combined steps of adding a shikimic acid high-purity product, performing high-temperature treatment, and allowing the mixture to stand at a low temperature in order to precipitate a shikimic acid precipitate, and recrystallizing the shikimic acid precipitate to obtain the shikimic acid extract product the shikimic acid content of which is 98% or above.