The morphology of the photoactive layer within organic solar cells (OSCs) plays a key role in determining device performance. In addition to the film forming conditions, miscibility between donors and acceptors critically derives the corresponding morphology, which can be empirically evaluated by the Flory–Huggins interaction (χ). Herein, a new non-fullerene acceptor (NFA) with long alkyl chains and fluorinated end groups, BTP-4F–C9-20, is reported, which has sufficient solubility in common solvents and good miscibility with the polymer donor PM6. PM6:BTP-4F–C9-20 binary OSC achieved a maximum PCE of 16.5%, as a result of fine phase separation that creates abundant heterojunctions for exciton dissociation but insufficient bi-continuous pathways for charge transport. A chlorinated NFA Y7-BO with higher χ with PM6 is introduced into the PM6:BTP-4F–C9-20 host system, which increases phase separation with slightly enlarged domains to better shape the charge transport pathways. The PM6:BTP-4F–C9-20:Y7-BO (1:1.1:0.1) ternary OSC achieved a higher PCE of 17.3%, although Y7-BO provides limited complementary light absorption. This work demonstrates that the Flory–Huggins interaction is an effective parameter to fine tune the morphology of ternary OSCs to promote photovoltaic performance.