A comprehensive lipidomic analysis was performed onto three edible brown seaweeds, namely Laminaria japonica, Undaria pinnatifida, and Scagassum natans, using reversed-phase liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (RPLC−Q-TOF-MS/MS). In total, 675 lipid molecules, including glycolipids (GLs), phospholipids, sphingolipids (SLs), betaine lipids, and glycerolipids, were identified and semiquantified. With the exception of the high content of diacylglycerols found in L. japonica (54.6% of total lipids), GLs were the dominant component in the three brown seaweeds (27.7−56.7% of total lipids), containing a high proportion of eicosapentaenoic acid. Interestingly, SLs represented by ceramide and hexosylceramide containing phytosphingosine and α-hydroxy fatty acid structures were detected in the three brown seaweeds. A large number of acylated GLs were identified and reported for the first time in these seaweeds, including acylated monogalactosyldiacylglycerol and acylated digalactosyldiacylglycerol containing nonoxidized fatty acids. The bioactive lipids identified herein could be considered potential biomarkers for identifying these seaweeds, evaluating their nutritional value and further promoting their utilization.