A design concept of "side chain isolation" was proposed for developing new polythiophene derivatives with conjugated side chain (CSC-PTs), and PTSTPA with styryl triphenylamine (TPA) side chain and unsubstituted tetrathienyl spacer was designed and synthesized. Compared to previously reported CSC-PTs, side chain isolated PT5TPA showed red shifted and enhanced pi-pi* transition absorption of the polymer backbone along with the shoulder peak and steep absorption edge, indicating improved planarity of the backbone. In addition, the unsubstituted thiophene spacer along the polymer backbone of the side chain isolated PTSTPA results in a lower HOMO energy level of the polymer at 5.1 eV. The polymer solar cell based on PT5TPA as donor and indene-C(60) bisadduct as acceptor displayed a power conversion efficiency of 3.6% with a high open circuit voltage of 0.94 V, under the illumination of AM1.5G, 100 mW/cm(2). The results indicate that the side chain isolated CSC-PTs could open a new way for developing high performance photovoltaic polymers.