Gangliosides, a kind of acid glycosphingolipid containing sialic acid, plays a very important physiological role in biomembrane as one of the important components of neurocyte membrane. They were extracted from bovine brain by the Folch method and purified by silica gel and DEAE-Sephadex A-25 column chromatograph. Their molecular functional groups and microstructures of polymeric aggregates were studied by infrared spectrum(IR), ultraviolet spectrum (UV)and atomic force microscope (AFM). The experimental results indicate that: 55.2 mg of Gls from 100 g of wet bovine brain had a certain purity, 62.84%. And their UV absorption spectra appeared at 195 nm, near to the results reported by other peoples. Compared with the IR spectra of sialic acid, the experimental results showed that the structures of the products had the units of sialic acid. In order to investigate the aggregate structures of ganglioside. AFM technique was applied in water, and the results showed that gangliosides can form spherical or ellipsoidal structures in water. It was determined that the size of polymeric aggregates of gangliosides varies between 55 and 380 nm, the average size is (148.9±66.7) nm; the height is between 1.0 and 5.0 nm, and the average height is (3.25±1.01) nm. The experimental results provide a theoretical and experimental basis for investigating biological activity and the exploitation and utilization of neural drugs.