The invention discloses a molecular imaging method based on a high-stability capillary electrophoresis separation analysis technology, and relates to multiple fields of analytical chemistry, life science, clinical medicine, medicine development, material science and the like. The molecular imaging method comprises the steps of sample pretreatment, high-stability capillary electrophoresis sample introduction, separation and analysis and molecular distribution image drawing. The sample pretreatment adopts a grid knife method, and comprises the steps of uniform segmentation, in-situ extraction, enrichment, derivation and the like. According to the method, the strong separation capability and abundant separation modes of capillary electrophoresis are utilized, imaging elements are abundant, and neutral molecules difficult to distinguish by mass spectrometry and components with the same mass-to-charge ratio can be imaged. The batch processing capacity of capillary array electrophoresis can accelerate the separation process and shorten the imaging analysis time. By means of the high-stability capillary electrophoresis technology, the peak position of the separated component can be stabilized, identification and positioning of the component are facilitated, and then a spatial distribution image of the stable peak component is constructed.