AbstractNonfullerene small‐molecule acceptors (SMAs) are considered as a key component of next‐generation organic photovoltaics. Introducing functional groups to the end‐groups of “acceptor‐donor‐acceptor”‐type SMAs is a facile and convenient way to tune their optoelectronic and morphological properties. Here, molecular dynamics simulations are combined with long‐range corrected density functional theory calculations to explore the molecular‐scale impact that the position of methoxy substitution in the end‐group has on the molecular packing and electron‐transfer properties in neat films. The focus here is on 3,9‐bis(2‐methylene‐(3‐(1,1‐dicyanomethylene)‐indanone))‐5,5,11,11‐tetrakis(4‐hexylphenyl)‐dithieno [2,3‐d:2′,3′‐d′]‐s‐indaceno[1,2‐b:5,6‐b′]dithiophene (IT‐OM), where three end‐group methoxy substitution positions are evaluated. Changing the methoxy substitution position is found to influence, to different extents, the planarity of the end‐groups and thus the intermolecular packing density. The effect on the intermolecular electron‐transfer rates is also examined and leads to markedly different sizes of strongly interconnected clusters. Overall, these findings are fully consistent with the experimental evolution of electron mobility in the neat IT‐OM film as a function of methoxy substitution position.