We employed the quantum mechanical (QM) and all-atom molecular dynamics (AAMD) simulation methods to examine the correlation between the molecular conformation and the UV-visible absorption behaviors of two-dimensional thiophene-based conjugated polymers. We focus on the effects of molecular regioselectivity and the presence of conjugated side chains. First, when the conjugated thiophenes exist only along the main chains, the ordered molecules of 100% HT (P3HT) and 100% HH/TT (PDBT) tend to keep a coplanar trans conformation due to the pi-pi attractions. The resultant UV-vis absorption spectra show one peak in the visible range, and a significant red-shift with the increasing of molecular weight. When substituting the hexyl side chains with the hexylthiophenes, the 100% HT PD3QT and 100% HH/TT PD4QT in the ordered state exhibit quite different absorption features. The simulated spectrum of PD4QT in the ordered state has the characteristics of two absorption peaks. While the spectrum of ordered PD3QT shows one absorption peak with the wavelength range between the two peaks of the ordered PD4QT. These absorption results are strongly correlated with the conformation behavior of the conjugated thiophenes along the side chains and main chains. In the disordered solution state, due to the lack of pi-pi interactions, the effective conjugation length for the more coil-like chains can only be extended up to 3-5 monomers regardless of the molecular weight. Molecular regioselectivity has little influence on the UV-vis absorption behavior in the solution state. Our simulated results for P3HT in the ordered and disordered states have been shown in good agreement with the experimental results. (C) 2013 Elsevier Ltd. All rights reserved.