Wheat is the staple food for the world’s major populations. However, chemical characters of geographically authentic wheat samples, especially for the lipids, have not been deeply studied. The present research aimed to investigate lipid compositions of Chinese wheat samples and clarify the major markers that contribute to the geographical differences. A total of 94 wheat samples from eight main wheat-producing provinces in China were evaluated to differentiate their lipid compositions. Based on the data collected from ultra-high-performance-liquid-chromatography tandem time-of-flight mass spectrometry (UPLC-Q/TOF MS), an optimized non-targeted lipidomic method was utilized for analyses. As the results, 62 lipid compounds, including fatty acids, phospholipids, galactolipids, triglycerides, diglycerides, alkylresorcinol, and ceramide were tentatively identified. Partial least squares discriminant analysis (PLS-DA) demonstrated a more satisfying performance in distinguishing wheat samples from different origins compared with principal component analysis (PCA). Further, the abundances of triglycerides and glycerophospholipids with more unsaturated fatty acids were found greater in wheat samples from northern origins of China, while more glycolipids and unsaturated fatty acids arose in southern original wheat samples. These findings describe the lipid profiles of wheat samples in China and could contribute to the quality and safety control for the wheat flour products.