Reportedly, proteins involved in lipid metabolism change significantly in the jejunal crypt cells of early-weaned piglets, but the exact lipid profile change remains uncertain. In the present study, 32 piglets weaned at 21 d of age were randomly divided into 4 groups with 8 replicates. The jejunal crypt cells of a group of piglets on the post-weaning day (PWD) 1, 3, 7, and 14 were isolated per time point. Crypt cell lipid profiles were analyzed using ultra-high-performance liquid chromatography coupled with hybrid quadrupole time-of-flight mass spectrometry. This study showed that piglets suffered the greatest weaning stress on PWD 3 in terms of the lowest relative weight of the small intestine, the highest relative weight of the spleen, and the highest levels of malondialdehyde, cholesterol, and low-density lipoprotein cholesterol. The lipid profile of jejunal crypt cells including carnitine, sulfatide, sphingomyelin, hexosylceramide, and ceramide greatly changed after weaning, especially between PWD 3 and 14 (P