Despite the versatile processibility of three-dimensional CH8 series acceptors used in efficient organic solar cells (OSCs), understanding the relationship between the linkage units and performance has been significantly challenging. To address this, we present two dimeric acceptors, CH8-8 and CH8-9, which utilize 3,4-ethylenedioxythiophene and 3,4-dimethoxythiophene as linkage units, respectively, to investigate their effects on molecular properties and device performance. CH8-9 with 3,4-dimethoxythiophene as the central linker exhibited a larger dihedral angle of 37.2 degrees than CH8-8 (23.3 degrees), which is beneficial for avoiding over-aggregation and thus forming a more ideal morphology. Consequently, the morphology of CH8-9 showed a more uniform and smoother surface, leading to enhanced charge transport with more balanced charge-transport mobilities. The resultant PM6:CH8-9-based devices displayed a higher fill factor (FF) and short-circuit current density (Jsc), which led to a higher power conversion efficiency (PCE) of 16.3%, surpassing the PCE of the PM6:CH8-8-based device. Our work provides a comprehensive analysis of the impact of incorporating dioxane- and methoxy-substituted thiophene units on device performance, offering insights into optimizing linkage units in multi-dimensional molecules to improve the photovoltaic performance of OSCs.