Twisted benzodiperylenediimides (TBDPDI) with large rigid conjugated core and strong absorption is regarded as an excellent acceptor in non-fullerene solar cells. Since side chains of semiconductors play a crucial role in the solar cells, TBDPDI acceptors with different side chains (1-ethylpropyl, C5; 2-ethylhexyl, C8; 1-pentylhexyl, C11; 2-octyldodecyl, C20; 1-undecyldodecyl, C23) were synthesized. In solution, TBDPDI compounds (C5, C11, and C23) with alkyl chains branched at 1-position show significantly different absorption profiles and fluorescence intensity with those (C8 and C20) branched at 2-position, due to stronger aggregation of the latter. Nevertheless, alkyl chains have little effect on the molecular orbital energy levels and optical band gaps, as verified by cyclic voltammetry and solid state absorption. Due to their complementary absorption and matchable energy levels with donor of PCE10, these acceptors and PCE10 were used together to fabricate bulk heterojunction (BHJ) solar cells. Because of inferior phase separation with large domain size around 100 nm and bulky insulated side chains, acceptors (C20 and C23) with long alkyl chains have the low electron mobility (μe) around 10−8 cm2 V−1 s−1 and the low power conversion efficiency (PCE) of solar cells. TBDPDI (C11) with 1-pentylhexyl gives the highest PCE of 5.0% under the optimized condition, which is attributed to proper phase separation with domain size around 20 nm and highest μe of 10−6 cm2 V−1 s−1.