Membrane proteins are indispensable for cell signaling, bioenergetics, and transportation. Atomic structures of membrane proteins have been elucidated by methods in structural biology (e.g. X-ray crystallography). Structural changes of them in action should be investigated to improve the understanding of the molecular mechanisms in more detail. Infrared spectroscopy is a powerful method to analyze structural changes of protein by combining it with various kinds of stimulus-induced difference spectroscopic techniques. In this review article, my recent studies on microbial rhodopsin, ion channel and ion pump proteins are summarized. Light-induced difference infrared spectroscopy revealed the hydrogen-bonding change of Thr204 in pharaonis phoborhodopsin upon photoisomerization of the retinal chromophore, which turned out to be a key residue for the signal transduction. Attenuated total reflection (ATR) method was applied on the studies of ion-protein interaction of a potassium channel, KcsA, and a sodium pump, V-type ATPase. Finally, development of a rapid-buffer exchange apparatus for time-resolved ATR infrared spectroscopy is introduced, which would be a powerful technique for investigating ion- and ligand-binding reactions of membrane proteins.