Total glucocerebrosides of the sea cucumber Cucumaria frondosa (CFC) have been isolated from the less polar lipid fraction of the chloroform-methanol extract using high speed counter-current chromatography (HSCCC) with a two-phase solvent system composed of petroleum ether-methanol-water (5:4:1, v/v). Three glucocerebroside molecular species (CFC-1, CFC-2 and CFC-3) were isolated from crude total cerebrosides with repeated column chromatography. The structures of these three glucocerebroside molecular species were determined on the basis of chemical and spectroscopic evidence: fatty acids were mainly saturated (C22:0 and C18:0), monounsaturated (C24:1 and C20:1) and α-hydroxyl fatty acids (C24:1h, C23:0h, C23:1h and C22:0h), the structures of long-chain bases were dihydroxy (d17:1, d18:2 and d18:1) and trihydroxy (t17:0 and t16:0), and the glycosylation was glucose. High purity long-chain bases of sea cucumber Cucumaria frondosa (CF-LCB) were prepared from total lipids by HSCCC with a two-phase solvent system composed of n-hexane-methyl tert butyl ether-methanol-water (1:1:2:1, v/v). Compare with traditional preparative methods, the method of HSCCC is short cycle, high yield and less solvent consumption. The composition analysis of CF-LCB showed that the ratio of d18:2 and d17:1 was approximately 2:1. The four glucocerebrosides and long-chain bases from sea cucumber Cucumaria frondosa were evaluated for activity in vitro assays for the cytotoxic activities against Caco-2 colon cancer cells. The results indicated that both glucocerebrosides and long-chain bases exhibited an inhibitory effect on cell proliferation. Moreover, CFC-3 was most effective in four glucocerebrosides to Caco-2 cell viability. The inhibition effect of CF-LCB was much stronger than glucocerebrosides.