Threonine synthase (ThrS) catalyzes the final chemical reaction of l-threonine biosynthesis from its precursor, O-phospho-l-homoserine. As the phosphate ion generated in its former half reaction assists its latter reaction, ThrS is recognized as one of the best examples of product-assisted catalysis. In our previous QM/MM study, the chemical reactions for the latter half reactions, which are critical for the product-assisted catalysis, were revealed. However, accurate free energy changes caused by the conformational ensembles and entrance of water molecules into the active site are unknown. In the present study, by performing long-time scale MD simulations, the free energy changes by the divalent anions (phosphate or sulfate ions) and conformational states of the intermediate states were theoretically investigated. We found that the calculated free energy double differences are in good agreement with the experimental results. We also revealed that the phosphate ion contributes to forming hydrogen bonds that are suitable for the main reaction progress. This means that the conformation of the active site amino acid residues and the substrate, and hence, the tunable catalysis, are controlled by the product phosphate ion, and this clearly demonstrates a molecular mechanism of the product-assisted catalysis in ThrS.