The appearance of the A-DA1D-A type of non-fullerene acceptor Y6 and its derivatives significantly improves the power conversion efficiency of organic solar cells. However, the effects of the modulation of the side chains of Y6 on its morphology and charge transport in organic thin films are still not well understood. In this work, we have systematically studied the effects of symmetric modifications of the length of alkyl side chains and the types, such as branched or straight alkyl chains, and the introduction of heteroatoms to side chains on these properties. A multiscale study, including density functional theory and classical molecular dynamics simulations, has been used to answer this open question. We find that face-on configurations are generally dominant for the AA, A1A1, and DD stacking of molecular pairs. With respect to prototype Y6, the introduction of oxygen atoms to outer alkyl side chains could enhance AA stacking but worsen the electrical network and enlarge the reorganization energy during electron transfer, and changing outer side straight alkyl chains to branched chains ruins π-π stacking of all units significantly. Finally, we discover that shortening outer alkyl side chains appropriately or changing inner branched chains to straight chains with the same number of carbon atoms is a good strategy to improve the molecular π-π stacking and electron mobility of Y6 while changing outer straight side chains to branched chains or introducing oxygen atoms to outer straight chains is the opposite. This study provides a new insight into the relationship between morphology and electron mobility and will be helpful for the design of future high-performance non-fullerene acceptors.