Controlling the aggregation of small‐molecule acceptors (SMAs) is essential to obtain an optimal morphology and to improve the photovoltaic performance of polymer solar cells (PSCs). However, reducing intermolecular aggregation of SMAs is usually accompanied by the disruption of compact molecular packing thereby leading to their decreased electron mobilities. Here, two novel M‐series SMAs (MD1T and MD2T) based on ladder‐type heterononacenes with neighboring side‐chains separated by one or two thiophene rings are designed and synthesized. It is found that shortening the spacing of the neighboring side‐chains of the SMAs can greatly alleviate the intermolecular aggregation and alter the molecular orientation from bimodal edge‐on/face‐on to predominant face‐on while maintaining the compact molecular packing. As a result, a more favorable morphology with smaller domain sizes is formed for the MD1T‐based blend films, which greatly improves the charge generation and charge transport for the corresponding PSCs. The best‐performing MD1T‐based device affords an efficiency of 12.43%, over seven times higher than that of the MD2T‐based device. This work reveals the importance of the spacing between the neighboring side‐chains in modulating the molecular aggregation and active layer morphology, and the obtained structure‐performance relationships shall provide important guidance for designing highly efficient SMAs.