The invention discloses a preparation of secoisolariciresinol diglucoside, including steps of: ethanol extracting flaxseed meal in a soxhlet extraction device, wherein concentrated solution is obtained by decompress concentrating the extract; edulcorating the extract by acid precipitation and centrifugation; obtaining crude product of secoisolariciresinol diglucoside by alkaline hydrolysis, regulating PH value of extract, decompress concentrating and drying subsequently; product of secoisolariciresinol diglucoside with high content of SDG is obtained by ethanol extracting the crude product. The inventive production process is simple, easy to industrialize, totally avoid using toxic organic solution, and avoid using separation medium such as silica gel, macroporous resin, gelatin. The invention is capable of keeping effective elements of polyphenol in raw material, so as to ensure good medicine efficacy of subsequent product, while in favor of security of subsequent usage. The product can be used to improve osteoporosis, metabolism disorder of blood lipid, obesity, depression caused by women's climacteric syndrome, and to prevent and treat diseases related to heart, prostate, colonand kidney.