Oxygen reduction reaction (ORR) is a cathodic reaction in the fuel cell which is a promising candidate for clean energy conversion. To overcome the slow kinetics of ORR in the metal oxide catalyst, a novel concept of involving polypyrrole (pPy) has been developed. The pPy is identified as the co-catalyst to help catalysts to improve the efficiency in ORR. However, there have been only few theoretical studies on how pPy accelerates the ORR. Therefore, by using density functional theory (DFT) calculations, the effect of pPy on the ORR was studied with metal-doped terephthalate (M-TP) system. We used various metal (i.e., Co, Mn, Ni, Zn, Fe, and Cu) to generalize the effect of pPy. Without pPy, the rate determining reaction of M-TP systems was always the reaction *OOH → *O. However, when pPy was added, the secondary amine of pPy was calculated to be deprotonated during ORR to accelerate the reaction and recovered at the end. Through this study, we firstly suggested that the origination of the improved efficiency of ORR was the deprotonation and protonation of pPy.