The improvement of the power conversion efficiency (PCE) of polymer bulk heterojunction (BHJ) solar cells has generally been achieved through synthetic design to control frontier molecular orbital energies and molecular ordering of the electron-donating polymer. An alternate approach to control the PCE of a BHJ is to tune the miscibility of the fullerene and a semiconducting polymer by varying the structure of the fullerene. The miscibility of a series of 1,4-fullerene adducts in the semiconducting polymer, poly(3-hexylselenophene), P3HS, was measured by dynamic secondary ion mass spectrometry using a model bilayer structure. The microstructure of the bilayer was investigated using high-angle annular dark-field scanning transmission microscopy and linked to the polymer-fullerene miscibility. Finally, P3HS:fullerene BHJ solar cells were fabricated from each fullerene derivative, enabling the correlation of the active layer microstructure to the charge collection efficiency and resulting PCE of each system. The volume fraction of polymer-rich, fullerene-rich, and polymer-fullerene mixed domains can be tuned using the miscibility leading to improvement in the charge collection efficiency and PCE in P3HS:fullerene BHJ solar cells. These results suggest a rational approach to the design of fullerenes for improved BHJ solar cells.