Acetate is a central metabolite that plays a key role in almost all organisms, and acetate channels are often essential for their survival. Recently solved structures of the acetate channel Succinate-Acetate Permease (SatP) provide an atomic view of its closed state. However, the open state of the channel, the key residue conformational changes that trigger the channel to open, and the free energy barrier of acetate transportation remain elusive. To address these questions, we performed microsecond time scale molecular dynamics (MD) simulations and umbrella sampling. Several acetate passing events were observed in the MD trajectories with the application of an external electric field. Further analyses reveal the molecular mechanism of the channel opening, which results from the repacking of key residues, such as Gln50 and Phe17, as well as the subsequent outward movement of all transmembrane helices. Our simulations show that acetate is always surrounded by several water molecules when passing through the channel. Furthermore, a high energy barrier of 15 kcal/mol was observed from the free energy profile generated by umbrella sampling on the closed state of the channel. Our study deepens the understanding of the molecular mechanism of acetate transport through the channel SatP and is expected to facilitate the drug discovery on this target.