The molecular interactions between solvent and nanoparticles during photoactive layer formation in organic photovoltaic (OPV) cells influence the morphology of the photoactive layer and hence determine the power conversion efficiency. Prediction of optimal synthesis parameters in OPVs, such as choice of solvent, processing temperature, and nanoparticle concentration, requires fundamental understanding of the mechanisms that govern the agglomeration of nanoparticles in solvents. In this study, we used molecular dynamics simulations to simulate a commonly used organic nanoparticle, [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), in various solvents to correlate solvent-nanoparticle interactions with the size of the agglomerate structure of PCBM. We analyzed the effects of concentration of PCBM and operating temperature on the molecular rearrangement and agglomeration of PCBM in three solvents: (i) toluene, (ii) indane, and (iii) toluene-indane mixture. We evaluated the agglomeration behavior of PCBM by determining sizes of the largest clusters of PCBM and the corresponding size distributions. To obtain further insight into the agglomerate structure of PCBMs, we evaluated radial distribution functions (RDFs) and coordination numbers of the various moieties of PCBMs with respect to solvent atoms as well as with respect to that of other PCBMs. Our simulations demonstrate that PCBMs form larger clusters in toluene while they are relatively dispersed in indane, which indicates the greater solubility of PCBM in indane than in toluene. In toluene-indane mixture, PCBMs are clustered to a greater extent than in indane and less than that in toluene. To correlate agglomerate size to nanoparticle-solvent interactions, we also evaluated the potential of mean force (PMF) of the fullerene moiety of PCBM in toluene and indane. Our results also show that the cluster size of PCBM molecules increases with the increase of concentration of PCBM and the processing temperature. To correlate the PCBM agglomeration with the dynamics of solvents, we evaluated the rotational correlation functions of the solvents. Our results illustrate that toluene relaxes faster than indane in the simulated systems and relaxation time of solvent molecules decreases with the decrease of concentration of PCBM and increase of processing temperature. Results presented in this study provide fundamental insight that can help to choose favorable solvents for processing PCBMs in OPV applications.