Shaking-withering is a new technique in black tea manufacturing, which enables promoting aroma quality. Lipids are important tea aroma precursors. However, the lipids metabolism and its contribution to aroma formation of shaking-withering black tea (SBT) remain unknown. Herein, 436 lipids and 45 fatty acid-derived volatiles (FADVs) and their dynamic changes during SBT processing were investigated. Among them, 113 lipids and 29 FADVs (mainly floral/fruity fatty aldehydes and esters) were screened as critical compounds associated with shaking-withering. Key enzymes PLA, LOX and HPL showed enhanced activity/expression in SBT. Degradation of glycerophospholipids, glycoglycerolipids, and fatty acids were annotated as potential lipid metabolism pathways. Particularly, glycoglycerolipids containing 18:2, 18:3 fatty acyls, e.g., MGDG(18:2/18:3), DGDG(18:3/18:3), showed most predominate degradation after shaking and negative correlation with FADVs, and were highlighted as key potential aroma precursors in SBT. These results demonstrated that shaking may trigger greater glycoglycerolipids degradation and FADVs formation, contributing to SBT aroma improvement.