Hepatocellular carcinoma (HCC) accounts for the major primary liver cancer, and its morbidity and mortality rates are very high. Identification of novel biomarkers for the early diagnosis and treatment of this disease is of crucial importance. In this study, a continuous-flow normal-phase/reversed-phase two-dimensional liquid chromatography-quadrupole time-of-flight mass spectrometry (NP/RP 2D LC-QToF/MS) method was used to detect lipid species in human plasma from HCC patients and healthy controls. As a result, the two groups were clearly separated by principal component analysis. Besides, 23 lipid species with corrected p value \0.05 and fold change [1.5 were proposed as potential lipid biomarkers for HCC. Among them, 9 lipid species, including galactosylceramide (36:5), free fatty acid (20:4), phosphatidylethanolamine (40:6), phosphatidylethanolamine (38:6), diacylglycerol (40:5), diacylglycerol (44:2), lactosylceramide (40:3), phosphatidylcholine (40:6), and free fatty acid (22:5), exhibited excellent ability to distinguish HCC patients from healthy controls with the area under the receiver-operating characteristic curve [0.900, showing promising clinical value. Taken together, these results indicate the great potential of NP/RP 2D LC-QToF/MS method in disease diagnosis, which might be helpful in clinical practice.