Abstract: Lipidomics is an emerging discipline that uses modern analytical techniques to study lipid levels during disease development and treatment. It could be used to identify the pathways of lipid metabolism, build the network of lipid metabolism under normal or disease conditions, discover diagnostic biomarkers and monitor disease progression. Brain, the center system of organism, is the organ with the highest content of lipids. Disordered lipid metabolism could trigger a variety of brain diseases. Thus, comprehensive lipid profiling provides insight into the prevention and early diagnosis of encephalopathy. This paper focused on the recent advances and applications of lipidomics for brain diseases such as stroke, neurodegenerative disease, brain trauma, and brain tumor, aiming to provide reference for disease prevention and treatment.