Lipids are vital cellular constituents in plant, and lipid peroxidation metabolites are critical defence substances in plants. In this study, mass spectrometry along with projections to latent structures discriminant analysis (PLS-DA) was used to detect lipid metabolism changes in Arabidopsis thaliana in response to oligochitosan (an effective resistance elicitor for the control of plant diseases). The PLS-DA showed that lipid metabolites of Arabidopsis thaliana were influenced by oligochitosan treatment. The total content of oxylipin containing monogalactosyldiacylglycerols, oxylipin-containing digalactosyldiacylglycerols, and oxylipin-containing phosphatidylglycerols increased firstly (after 1 h), and then decreased with the increase of oligochitosan treatment duration. In contrast, the total content of monogalactosyldiacylglycerols, phosphatidylcholines, phosphatidyl-ethanolamine, and phosphatidylglycerols decreased firstly, and then increased with the increase of oligochitosan treatment duration. The amounts of free fatty acids (C16:2, C16:3, C18:2, and C18:3) were lower after treatment with oligochitosan for 1, 3, and 6 h than in the control, while the production of volatile organic compounds such as 2-hexenal (except for 3 h) and nonanal was higher than in the control. In conclusion, lipid metabolites of Arabidopsis thaliana were influenced by oligochitosan treatment, and the synthesized lipids and oxylipin-containing lipids were remodelled and free fatty acids was metabolized to volatile organic compounds.