A series of end-functionalized poly(3-hexylthiophene)s (P3HTs) were synthesized by end-capping with electron-deficient moieties (EDMs, oxadiazole (OXD) and triazole (TAZ)) to prevent the negative influence of bromine chain ends in the common uncapped P3HT in polymer solar cell (PSC) applications. On the basis of the electron-withdrawing capability of the planar OXD end groups, P3HT-end-OXD relative to the uncapped P3HT exhibits a raised absorption coefficient, extended exciton lifetime, and increased crystalline order in the blend with PCBM, leading to an effectual improvement in photovoltaic parameters. However, P3HT-end-TAZ has an opposite result even worse than that of the uncapped P3HT, arising from bulky TAZ end groups. As a consequence, P3HT-end-OXD gives a power conversion efficiency (PCE) of 4.24%, which is higher than those of the uncapped P3HT (3.28%) and P3HT-end-TAZ (0.50%). The result demonstrates that the EDM modification is a valuable method to tailor the structural defect of polymer chain ends. However, the efficacy is dependent on the structure of EDM.