The high power conversion efficiency of bulk heterojunction (BHJ) polymer solar cells can be achieved from either low crystallinity (P3TI) or high crystallinity (P6TI) of isoindigo-based donor–acceptor alternating copolymers blended with PC₇₁BM by controlling nanophase separation using additives. P3TI shows similar device performance regardless of the type of additives, while P6TI is significantly affected by whether the additive is aliphatic or aromatic. To understand the interplays of crystallinity of polymers and the type of additive on the formation of nanomorphology of BHJ, we employed the simultaneous grazing-incidence small- and wide-angle X-ray scattering (GISAXS and GIWAXS) technique to perform the quantitative investigation. By incorporating additives, the PC₇₁BM molecules can be easily intercalated into the P3TI polymer-rich domain and the size of the PC₇₁BM clusters is reduced from about 24 nm to about 5 nm by either aliphatic 1,8-diiodooctane (DIO) or aromatic 1-chloronaphthalene (CN). On comparison, it is found to be more difficult for PC₇₁BM molecules to be intercalated into the highly crystalline P6TI dense domain, and the PC₇₁BM molecules have a higher tendency to be self-aggregated, which results in a larger size of PC₇₁BM clusters of about 58 nm. The clusters can be reduced to about 7 nm by DIO and 13 nm by CN. The presence of crystallites in the P6TI domain can interact with the additive to tailor the crystallization of PC₇₁BM clusters to a size similar to that of P6TI crystallites (∼12 nm) and form a connected network for efficient charge transportation. Thus, the power conversion efficiency of P6TI:PC₇₁BM reaches its maximum of 7.04% using aromatic CN additives. This is a new finding of the effect of crystallinity, which is not observed in the common low crystalline donor–acceptor alternating copolymers such as PTB7. Our results provide a useful guideline to manipulate the desired morphology of BHJ films constructed from alternating copolymer with different crystallinity, which is critical for achieving high power conversion efficiency of solar cells.