Infrared spectroelectrochemistry was employed to study the deactivation polythiphene films in acetonitrile in this paper. Electrochemical experiments indicated that the deactivation of polythiophene films impedes charge transfer in the films. Infrared spectra showed the structural change of the films during the deactivation. Nucleophilic additives in the solution accelerate the film deactivation. The stronger the nucleophiles, the faster the polymer deactivates. The reason for the film deactivation is attributed to the decomposition of the polymer under the attacks from the both the nucleophilic additives and solvent. Mechanism of the deactivation under different conditions have been discussed.