Efficient light absorption in thin-film photovoltaic (PV) devices is crucial for improving their efficiency and reducing cost. Here we have not only developed a low-cost and scalable method to fabricate a unique type of integrated-nanopillar-nanowell (i-NPW) structure by integrating nanopillar and nanowell arrays together vertically, but also demonstrated the attractive optical property of the i-NPW arrays by leveraging the advantages of "positive" and "negative" nanostructures for photon harvesting. Impressively, the 2 μm thick i-NPW arrays with only 40 nm a-Si coating obtained a day-integrated absorption of 89.27%, as opposed to only 33.45% for the planar control sample. These results suggest the feasibility and clear advantage of vertical integration of three-dimensional (3-D) nanophotonic structures, and meanwhile also pave a viable and convenient way toward a 3-D ultrathin film PV module with potency for high energy conversion efficiency.