The molecular interactions in poly (N-isopropylacrylamide) (PNIPAAM) aqueous solution have been quantitatively investigated by using a newly developed thermal micro attenuated total reflection/Fourier transform infrared (ATR/FT-IR) spectroscopic system. PNIPAAM was prepared by the w/o emulsion method and its lower critical solution temperature (LCST) was examined by cloud point measurement and differential scanning calorimetry. The LCST of this PNIPAAM in water was about 33 degrees C, which was also confirmed by this thermal micro ATR/FT-IR spectroscopic system. Using this novel spectroscopic system with curve-fitting program, we found that below the LCST the molecular structure of PNIPAAM in water exhibited a predominantly intermolecular hydrogen bonding (about 50%-70% of total molecular interaction estimated from amide I band) between PNIPAAM and water. However, above LCST the intramolecular hydrogen bonded conformation was about 70% in total molecular interaction (estimated from amide II band). Moreover, the hydrophobic interaction of methyl group in PNIPAAM molecule increased 1.5 times when the temperature was above the LCST. The results quantitatively indicate that the intermolecular interactions might occur mainly between PNIPAAM molecules and water when temperature was below the LCST. When the temperature was above the LCST, however, PNIPAAM molecules in water were aggregated due to both the intramolecular interactions within PNIPAAM molecules and the hydrophobic interactions in system.