Nanometer scale cobalt thin films of different structures and thicknesses supported on glassy carbon were prepared by electrochemical deposition under cyclic voltammetric conditions (denoted nm-Co/GC(n)). The thickness of Co thin films was altered systematically by varying the number (n) of potential cycling within a defined potential range in electrodeposition. Electrochemical in situ scanning tunneling microscopy (STM) and ex situ scanning electron microscopy (SEM) were employed to characterize the surface structure of Co thin films. It has been illustrated that the Co thin films were uniformly composed of Co nanoparticles, whose structure and size varied with increasing n. The structure of nanoparticles inside the Co thin films underwent a transition from bearded nanoparticles to multiform nanoparticles and finally to hexagonal nanosheets, accompanying with an increase of average size. In situ FTIR reflection spectroscopic studies employing CO adsorption as probe reaction revealed that the Co thin films all exhibited anomalous IR properties; that is, along with their different nanostructures they presented abnormal IR effects, Fano-like IR effects, and surface-enhanced IR absorption effects. CO adsorbed on Co thin films dominated by bearded nanoparticles yielded abnormal IR absorption bands; that is, the direction of the bands is inverted completely, with enhanced intensity in comparison with those of CO adsorbed on a bulk Co electrode. The enhancement of abnormal IR absorption has reached a maximal value of 26.2 on the nm-Co/GC(2) electrode. Fano-like IR features, which describe the bipolar IR bands with their positive-going peak on the low wavenumbers side, were observed in cases of CO adsorbed on Co thin films composed mainly of multiform nanoparticles, typically on the nm-Co/GC( 8) electrode. IR features were finally changed into surface-enhanced IR absorption as CO adsorbed on the nm-Co/GC(30) electrode, on which the Co thin film is dominated by Co hexagonal nanosheets.