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This study evaluated the effects of long-chain bases from sea cucumber (SC-LCBs) on modulation of the gut microbiota and inhibition of obesity in high fat diet-fed mice. Results showed that SC-LCBs exerted significant antiobese effects, which were associated with the inhibition of hyperglycemia and lipid accumulation. SC-LCBs also regulated serum adipocytokines toward to normal levels. SC-LCBs caused significant decreases in Firmicutes, Actinobacteria phylum, and obesity-related bacteria (<i>Desulfovibro</i>, <i>Bifidobacterium</i>, <i>Romboutsia</i> etc. genus). SC-LCBs also elevated Bacteroidetes, Proteobacteria, Verrucomicrobia phylum, and short chain fatty acids (SCFAs)-producing bacteria (<i>Bacteroides</i>, <i>Lactobacillus</i>, <i>Lachnospiraceae_NK4A136_group</i> etc. genus). Moreover, serum and fecal lipoplysaccharide (LPS) concentrations and its dependent toll-line receptor 4 pathway were inhibited by SC-LCBs treatment. SC-LCBs caused increases in fecal SCFAs and their mediated G-protein-coupled receptors proteins. These suggest that SC-LCBs alleviate obesity by altering gut microbiota. Thus, it sought to indicate that SC-LCBs can be developed as food supplement for the obesity control and the human gut health.