Germination, a new processing technology, is widely used to improve the nutritional value of plant seeds. Cereals and legumes sprouts are widely popular around the world. In this study, a novel form of sprouts-based rapeseed was produced. Germination promoted the degradation of phytic acid and glucosinolates (GLs) in rapeseed. On the fourth day of germination, the degradation rate of phytic acid in rapeseed was nearly 80%, and the degradation rate of GLs reached more than 90%. The changes in lipid species and content by sprouting were assessed. The crude fat content was significantly reduced during rapeseed germination. Using non-targeted lipidomics, three hundred eighty-nine lipid molecules in 4 categories and 17 subclasses were identified in rapeseed/rapeseed sprouts. Glycerides were most abundant, followed by fatty acids, glycerophospholipids, and sphingolipids. Germination affected not only the lipid content but also its composition. Some functional lipids (such as FAHFAs) were generated and enriched during germination. The content of monounsaturated fatty acids first raised and then decreased during germination. The finding will serve as a theoretical reference for developing novel sprouts based on rapeseed, furnish primary data concerning the nutritional content of rapeseed sprouts, and provide fresh ideas for rapeseed resource exploitation.