Self-assembly is crucial for small molecular organic solar cells, which are extremely sensitive to the molecular structure. In this work, three subtle structural changed end-capped acceptors with increased electron withdrawing ability, named octyl 2-cyanoacetate (=CNCOOC8H17), 3-oxoundecanenitrile (=CNCOC8H17), and 2-(octylsulfonyl) acetonitrile (=CNSOOC8H17), were synthesized and introduced into a planar conjugated backbone using ethylhexyl-thiophene substituted benzodithiophene (TBDT) as a core and trithiophene as a π-bridge (labelled M1, M2 and M3, respectively). Their effects on absorption, thermal properties, and morphologies were studied and compared. In particular, the molecular packing of the three materials varied significantly, and the hole mobilities differed by orders of magnitude. As a result, the fill factors of devices varied from 52% to 72%. Combining the effects of electron-withdrawing capability and molecular packing, the power conversion efficiencies of the optimized devices increased from 3.0% for M3 to 6.4% for M1 and M2. The relationship between end-capped acceptors and photovoltaic properties would generate valuable insights into further producing more efficient solution-processable organic solar cells.