A study of poly(3-hexylthiophene) (P3HT) thin films by spin-coating process, deposited on conducting glass substrates of fluorine-doped tin oxide (FTO), is performed varying thicknesses from 32 to 80 nm. We observe an increase in absorbance at 510, 550, and 610 nm; however, for film thicknesses between 40 and 50 nm, the spectra show abnormalities below 500 nm, resulting from the creation of defects that modify the bandgap value. To prove this hypothesis, we determine the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy level positions of different thickness P3HT films by energy-resolved electrochemical impedance spectroscopy (ER-EIS). This experiment revealed that the HOMO level remains constant regardless of the film thickness, whereas the LUMO exhibits a thickness dependence, where the 46 nm film produces a maximum. To analyze the potentiostatic EIS response, we propose an equivalent electric circuit (EEC) to build relative influence diagrams. The corresponding numerical analysis provides, first, a technique to select ER-EIS appropriate frequencies for studying the electronic response of P3HT films, and second, it allows identifying film defect states in the gap region: density of states (DOS) near the HOMO and LUMO levels, and defect states inside the gap. A molecular dynamics force field (FF) simulation provides a distribution of geometrical arrangements of P3HT oligomers, which are studied subsequently by density functional theory (DFT) calculations to estimate their HOMO-LUMO energies variations. These calculations allow us to explain DOS features detected experimentally near the gap borders.