Polymer solar cells, which convert clean renewable solar energy into electricity, have been considered as most promising technology. It is well recognized that the power conversion efficiency of the cell device greatly depends on the morphology of the polymer active layer, and the post-treatments commonly used, such as energy consuming thermal annealing and solvent vapor treatment, are not suitable for commercial applications on large-area polymer solar cells. Herein, we propose a facile aqueous solution post-treatment, which involves only water and a small amount of carbon disulfide (0.13 wt% of CS2), based on regioregular poly (3-hexylthiophene) (P3HT) and [6, 6]-phenyl-C61-butyric acid methyl ester (PCBM) blend film to improve the active layer morphology and increase the device efficiency. Upon soaking the blend film in the aqueous solution, P3HT crystallinity is increased and an optimum morphology of nanoscale phase separation with an interpenetrating network is constructed, which offers percolating pathways for charge carrier transport. Furthermore, AFM and XPS analyses reveal that a coarser structure with heave-like PCBM-rich domains is built up at the active layer/cathode (top) interface, which improves the contact with the metal cathode for efficient electron transportation and collection. The feasibility of this method is verified by J–V characteristic of the photovoltaic device, which demonstrates an increased PCE of 3.09% compared with 1.84% of the pristine device, indicating its potential implementation on the application of large-area polymer solar cells.