The electronic structure and properties of 3,4-ethylenedioxythiophene (EDOT) based alternating donor-acceptor conjugated copolymers and their model compounds were studied by the density functional theory (DFT) at the B3LYP level with 6-31G or 6-31G** basis set. The acceptors investigated include thiazole (Z), thiadiazole (D), thienopyrazine (TP), thienothiadiazole (TD), thiadiazolothienopyrazine (TPD), quinoxaline (BP), benzothiadiazole (BD), pyrazinoquinoxaline (BPP), benzobisthiadiazole (BDD), and thiadiazoloquinoxaline (BDP). The torsional angle, intramolecular charge transfer, bridge bond length, and bond length alternation were analyzed and correlated with the electronic properties. It was found that the geometries of the donor-acceptor materials were significantly affected by the ring size and intramolecular charge transfer. The HOMO level, LUMO level, and band gap of the model compounds were well correlated with the acceptor strength. However, the electronic properties of the copolymers did not vary systematically with the acceptor strength due to the change in geometry from model compound to polymer. The aromatic geometry of EDOT-TP model compound is transformed to quinoid in the corresponding copolymer and results in a small band gap (E-g) of 0.97 eV. Large intramolecular charge transfer and the small bond length alternation in the EDOT-BDP copolymer resulted in an E-g of 0.7 eV. Hence, these two polymers could have potential applications for transparent conductors or photovoltaic devices. The small effective masses and large HOMO and LUMO bandwidths of PEDOT-TP and PEDOT-BDP make them potential materials for ambipolar thin film transistors. The theoretical results suggest that both the acceptor strength and the stable geometry contribute significantly to the electronic properties of alternating donor-acceptor conjugated copolymers.