Direct observation of the molecular structural change during chemical reactions including transition states is desirable to fully clarify the mechanism of chemical reactions. Time-dependent frequency variations in molecular vibration modes reflect structural change in transition states. Ultrafast changes in molecular structure during bond breaking and bond reformation can be clearly visualized using ultrafast spectroscopy. This study elucidated molecular structural information in states along the chemical reaction including transition state in the proton transfer of indigodisulfonate salt. The photoexcited proton transfer was found to follow a stepwise pathway. The monoalcohol intermediate generated by the proton transfer was found to return immediately to the original indigo without protontransfer configuration. This back reaction of this is the reason for the ultra-photostability of indigo over extremely long exposure to light. This shows that real-time vibrational spectroscopy by a few femtosecond pulse laser enables the observation of dynamic behavior of molecular vibrations during chemical reactions, leading to the clarification of reaction mechanisms or the development of new chemical reactions.