Goji berries, an important medicinal and edible plant, possess substantial medicinal and economic potential. While research has extensively investigated the polar metabolites of goji berries, their lipid metabolism has received comparatively less attention. Here, we performed comprehensive lipid profiling of 78 goji berry samples using UPLC-MS. We identified a total of 180 lipid compounds, classified into five classes: glycerolipids, glycerophospholipids, glycoglycerolipids, sphingolipids, and pigments. The data reveal the natural variation and accumulation patterns of lipid compounds in cultivated and wild goji berries, and assess lipid distribution characteristics across different harvesting periods and maturation stages. Heatmap clustering and PCA analysis indicated that all samples displayed a notable spatial aggregation. Furthermore, the OPLS-DA analysis demonstrated key markers for distinguishing goji berries from different harvesting periods. These findings offer valuable insights into the lipid metabolism in Lycium and establish a basis for assessing the quality of this genus.