We demonstrate that conjugated polymers (CPs)-based flexible solar cells with well-defined interdigitated donor-acceptor interfaces enhance charge separation and transport. The welldefined straight donor-acceptor interfaces are achieved successful application of nanoimprinting technology to rationally designed energy harvesting and hole transporting conjugated polymers. Nanoimprinting enables the precise and direct nano-scale control of the shape of the donoracceptor interface on both rigid and flexible substrates. Comparison between the performances of the solar cells having imprinted different feature sizes revealed that the short circuit current can be systematically increased by the interfacial area of the heterojunction without affecting the open circuit voltage. The results also showed that the vertically oriented heterojunction facilitate charge transport and allow synergistically improved fill factor, open circuit current, and ensuing energy conversion efficiency beyond the gain of the interfacial area of the heterojunction.