Camellia oleifera Abel. is an evergreen oil-bearing tree and widely cultivated in China. Camellia oleifera oil is considered to be a healthiest edible oil. However, the lipid profile are not well studied and ultilized. In the current study, we firstly used non-targeted LC-MS/MS method to describe the lipid profiles of two C. oleifera cultivars. Stringent criteria was used to screen significantly different lipids metabolites (SDLs). By comparing CL3 with CL5, 79 SDLs in CL3 were found to be significantly up-regulated, and 61 SDLs were found to be significantly down-regulated. Correlation analysis indicated that intra-category and inter-category correlation of glycerolipids and glycerophospholipids were strong in CL3 and CL53 cultivars. Through pathway enrichment analysis, we found that the most influential pathway in two cultivars was the glycerophospholipid metabolism pathway. The present results provide essential insights into lipid composition and a basis to make better ultilization of the lipids.