The study investigates the impact of thionation on N,N'‐di(dodecyl)‐4,5,8,9‐naphthalene diimide (NDI) through computational methods such as density functional theory (DFT/TD‐DFT), quantum theory of atoms in molecules (QTAIM), and Landauer theory (LT). Thionation, involving the replacement of diamide oxygens with sulfurs in NDI, significantly enhances quantum‐electronic/thermoelectric properties. Computational analyzes of energy of frontier orbitals HOMO/LUMO, dipole moment, polarizability, first superpolarizability, UV spectrum, and cohesive energy show the superior performance of the thione structure (M2) compared to the pristine structure (M1). Thionation decreased the energy gap from 01.3 eV (in M1 structure) to 1.87 eV (in M2 structure). The absorption wavelength in the pristine structure (M1) is calculated to be 507 nm, which increased to 1067 nm after thionation (M2). Cohesive energy values for each of M1 and M2 structures are calculated as 12.76 and 12.89 Kcal mol−1, respectively, which indicates the improvement of stability after thionation. After connecting M1 and M2 to gold electrodes (Au‐M1‐Au and Au‐M2‐Au) and applying electric fields, the Au‐M2‐Au structure shows a lower energy gap, lower thermoelectric activity and higher conductivity at field intensities with higher than 140 × 10−4 (a.u.), indicating its use as a field‐effect molecular device (such as molecular wire or molecular switch).