Naphthalene diimide (NDI) dimers, NDI-Ph-NDI with a phenyl linker and NDI-Xy-NDI with a xylene linker, are designed and synthesized. The influence of the xylene and phenyl linkers on optical properties, electrochemical properties, morphology, and device performance is systematically investigated. Non-fullerene organic solar cells (OSCs) with NDI-Ph-NDI show poor device efficiency due to aggregation of polymer chains and/or NDI dimers caused by the highly planar structure of NDI-Ph-NDI. Although NDI-Xy-NDI is a non-planar structure, uniform surface morphology and weak bimolecular recombination lead to high power conversion efficiencies of 3.11%, which is the highest value in non-fullerene OSCs with NDI small molecules.