The present invention provides a preparation method of a cerebral nerve nutritional therapeutic composition and relates to the field of synthesis of oils and fats. Fatty acid triglyceride, conjugatedlinoleic acid glyceride and phytosterol are used as raw materials, the raw materials are subjected to transesterification with 435 lipase, IM lipase and DF15 lipase, cooling, decolorization, deodorization, distillation and fine-filtration are conducted, then emulsification, embedding and spray-drying are conducted to obtain dry powder, then the dry powder is mixed with phosphatidylserine, N-acetylneuraminic acid, beta-hydroxy-beta-methylbutyrate calcium, konjac glucomannan, a mangosteen extract, elderberries and yeast beta-glucan, and homogenizing is conducted to obtain the medium-long chain structure lipid composition. The technology is simple, convenient and inexpensive, and can produce precise nutritional composition suitable for clinical rehabilitation of diseases of stroke, Alzheimer's disease, depression, Parkinson's disease, epilepsy, etc.