Since charge separation in organic photovoltaics takes place between n- and p-type semiconductors, their interface should be maximized within the active layer, while charge percolation pathways to the electrodes should be ensured. One way to obtain an ideal and thermodynamically stable morphology is to covalently link n- and p-type semiconductors, provided a sufficiently high internal order is achieved. To this end, we have synthesized a perylene-quaterthiophene-perylene triad substituted with poly(isobutene) segments that induce order at the nanoscale via microphase segregation. Charge separation under selective illumination on the quaterthiophene or perylene moiety was investigated by steady state and transient absorption spectroscopy, and related to the molecular packing and phase morphology deduced from electron and grazing incidence X-ray diffractions. Photoluminescence was quenched due to charge separation within the triad. In solution, these charges quickly recombined, but were shown to have a longer lifetime in films, which is beneficial for charge collection in photovoltaic devices. We have also investigated whether alignment of the supramolecular aggregates affects the photophysics.