Three-dimensional (3-D) nanostructures have demonstrated enticing potency to boost performance of photovoltaic devices primarily owning to the improved photon capturing capability. Nevertheless, cost-effective and scalable fabrication of regular 3-D nanostructures with decent robustness and flexibility still remains as a challenging task. Meanwhile, establishing rational design guidelines for 3-D nanostructured solar cells with the balanced electrical and optical performance are of paramount importance and in urgent need. Herein, regular arrays of 3-D nanospikes (NSPs) were fabricated on flexible aluminum foil with a roll-to-roll compatible process. The NSPs have precisely controlled geometry and periodicity which allow systematic investigation on geometry dependent optical and electrical performance of the devices with experiments and modeling. Intriguingly, it has been discovered that the efficiency of an amorphous-Si (a-Si) photovoltaic device fabricated on NSPs can be improved by 43%, as compared to its planar counterpart, in an optimal case. Furthermore, large scale flexible NSP solar cell devices have been fabricated and demonstrated. These results not only have shed light on the design rules of high performance nanostructured solar cells, but also demonstrated a highly practical process to fabricate efficient solar panels with 3-D nanostructures, thus may have immediate impact on thin film photovoltaic industry.