AbstractChemical structure of small molecule acceptors determines their performance in organic solar cells. Multiscale simulations are necessary to avoid trial‐and‐error based design, ultimately to save time and resources. In current study, the effect of sp²‐hybridized nitrogen substitution at the inner or the outmost position of central core, side chain, and terminal group of small molecule acceptors is investigated using multiscale computational modelling. Quantum chemical analysis is used to study the electronic behavior. Nitrogen substitution at end‐capping has significantly decreased the electron‐reorganization energy. No big change is observed in transfer integral and excited state behavior. However, nitrogen substitution at terminal group position is good way to improve electron‐mobility. Power conversion efficiency (PCE) of newly designed acceptors is predicted using machine learning. Molecular dynamics simulations are also performed to explore the dynamics of acceptor and their blends with PBDB‐T polymer donor. Florgy‐Huggins parameter is calculated to study the mixing of designed small molecule acceptors with PBDB‐T. Radial distribution function has indicated that PBDB‐T has a closer packing with N3 and N4. From all analysis, it is found that nitrogen substitution at end‐capping group is a better strategy to design efficient small molecule acceptors.