In this work, we focused on the interaction between hydrogen bond acceptor (HBA) and hydrogen bond doner (HBD) in the binary mixtures. The results showed that Cl−anion plays a key role in the formation of DESs. Also, the structural stability of deep eutectic solvents based on fatty acids (FAs) and choline chloride (Ch+Cl−) at different ratios was investigated in water using molecular dynamics simulations. We observed that the interaction between the chloride anion and the hydroxyl group of the cation leads to the transition of HBA to the water-rich phase. These atomic sites have important rule in the stability of the eutectic mixtures based on FAs and Cl−anion. However, it seems that the binary mixtures with the mole percent at 30% of [Ch+Cl−] and 70% of FAs have more stability than other ratios.