Perylenediimide-based donor acceptor cooligomers are particularly attractive in plastic electronics because of their unique electro-active properties that can be tuned by proper chemical engineering. Herein, a new class of co-oligomers has been synthesized with a dyad structure (AD) or a triad structure (DAD and ADA) in order to understand the correlations between the co-oligomer molecular architecture and the structures formed by self-assembly in thin films. The acceptor block A is a perylene tetracarboxyl diimide (PDI), whereas the donor block D is made of a combination of thiophene, fluorene, and 2,1,3-benzothiadiazole derivatives. D and A blocks are linked by a short and flexible ethylene spacer to ease self-assembling in thin films. Structural studies using small and wide X-ray diffraction and transmission electron microscopy demonstrate that AD and ADA lamellae are made of a double layer of co-oligomers with overlapping and strongly pi-stacked PDI units because the sectional area of the PDI is about half that of the donor block. These structural models allow rationalizing the absence of organization for the DAD co-oligomer and therefore to draw general rules for the design of PDI-based dyads and triads with proper self-assembling properties of use in organic electronics.