Smilax glabra Roxb. (SG) is a well-known traditional Chinese medicine that has been extensively used as both food and folk medicine in many countries. Although many beneficial health effects of SG and its primary components have been reported, their action on adipocyte function remains unknown. In the present study, we investigated the effects of the total flavonoids from Smilax glabra Roxb. (SGF) on lipid accumulation in mouse 3T3-L1 adipocytes and further elucidated its potential mechanism using RNA-Seq transcriptome technique. Our results showed that SGF exposure significantly decreased the lipid droplet size and the levels of cellular free fatty acids, while triglyceride accumulation was not affected by SGF. Transcriptome analysis revealed that SGF induced the expression of genes involved in triglyceride storage, fatty acid β-oxidation and mitochondrial biogenesis. Furthermore, we also observed an increased cellular ATP level and mitochondrial mass after SGF exposure, indicating that SGF enhanced mitochondrial function. The other relevant transcriptional changes appeared to be involved in AMPK/PGC-1α signaling, inflammatory response, as well as PI3K/AKT and calcium signaling pathways, which might contribute to the beneficial metabolic effects of SGF on adipocyte function. The results of Western blotting confirmed that SGF could increase the phosphorylation of AMPK while decrease the phosphorylation of AKT in adipocytes. Altogether, our results provided novel information about the molecular mechanism responsible for the effects of SGF on fat storage in adipocytes and highlights the potential metabolic benefits of SGF on human obesity and its related chronic diseases.