Self-assembly of fullerene derivatives plays an important role in controlling photovoltaic performance of organic solar cells (OSCs). Herein, we have synthesized two covalently bonded phenyl substituted fullerene derivatives -N-Mtheyl-2-[2,5-bis (trifluoromethyl)phenyl] fullerenopyrrolidine (1) and N-Methyl-2-[2,4bis(trifluoro-methyl-6-methoxy)phenyl]fullerenopyrrolidine (2), which are employed as electron acceptors in OSCs. The self-assembly of two aforementioned molecules were investigated in the binary solvent system of chloroform and methanol (1:1 volume ratio). Further, optical, electro-chemical and micro-structural properties of self assembled structures were also studied. It is found that the architecture of assembly is directed by the functional groupsatthe phenyl ring and solvent molecule. The molecule 1 possessing -CF3 group and the molecule 2 possessing additional -OMe group on fullerene unitform flowers and flakes like structures, respectively. The assembly structure of 1 gets converted from flower to disc like structure with the variation of solvent from methanol to hexane. The OSCs fabricated using molecule 1 and molecule 2 as acceptor with PTB7 donor showed a power conversion efficiency of 6.8 and 3.6%, respectively with high open circuit voltages of ∼ 0.8 V.