Understanding the origin of different morphologies in bulk-heterojunction solar cells can provide effective guidelines to rational control of the morphologies in the active layer. Here, we have uncovered the importance of molecular interactions on the morphologies for not only donor materials but also for fullerene acceptors in organic solar cells through the multiscale coarse-graining molecular dynamic simulations at the real device level (∼83 nm × 83 nm × 83 nm). It is found that oligothiophene donors with polar end groups could not only facilitate the formation of continuous donor network but also promote the aggregation and connection of fullerenes toward efficient hole and electron transport. On the contrary, fullerenes are well dispersed at the molecule levels in the less polar oligothiophene matrix and thus contribute to the poor electron transport mobility and device performance, which is consistent with the observed differences in both morphology and charge transport properties of these two systems. These results would provide effective guidelines for the rational molecule design and morphology control to further enhance the device performance of organic solar cells.