Microscopic mechanism of phase transfer catalyst (PTC) is investigated by molecular dynamics simulation. As an example of PTC, tetrabutylammonium cation is treated which facilitates Cl - transfer from water to chloroform phase. Calculated free energy profiles reveal the effects of PTC in relation to the pertinent change of interface structure. The ion pair formation changes the free energy profiles in the late stage of transfer, where large structural fluctuation emerges, called water finger. The PTC controls the formation of water finger and thereby influences on the free energy. These microscopic insight is important for PTC-assisted reactions at the interface.