Supercritical fluid chromatography (SFC), which uses supercritical fluid with higher diffusivity and lower viscosity than liquid as its mobile phase, can provide fast, green, high-throughput and good performance methods for the analysis of complicated samples. It is an advantageous alternative for the separation of polar and nonpolar compounds, and even chiral isomers. As an important constituent of living organisms, lipids and the related lipidomics researches have attracted dramatic attention during the past years. The separation and identification of lipids and lipid isomers are of great significance and remain challenging. In this mini-review, the principle of SFC and its applications in lipid isomer separation are summarized.