The evolution of the structural and optical characteristics of polymorphic organic perylene nanoparticles (NPs) is demonstrated by controlling the pi-pi interactions using a hydrothermal process. The light-emission colors of the perylene NPs vary gradually from yellow to green to light blue with increasing hydrothermal temperature from 110 to 160 degrees C. An enhanced crystallinity of the NPs from 110 degrees C to a critical temperature T-c of 140 degrees C and a transition to the amorphous phase above T-c are observed. The evolution of the photoluminescence (PL) and optical-absorption characteristics in terms of variations in the crystallinity and physical dimensions (size and shape) of the perylene NPs resulting from the hydrothermal process are analyzed. These results are confirmed by nanoscale PL measurements for single NPs using laser confocal microscopy. The photovoltaic characteristics of organic solar cells (OSCs) are improved through the use of the perylene NPs. It is found that the performance of the OSCs is strongly correlated with the optical-absorption properties of the perylene NPs.