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.