The intramolecular electronic couplings in organic mixed-valence systems [D-(ph)(n)-D](center dot+) (D = 2,5-dimethoxy-4-methylphenyl, n = 0, 1, and 2) are calculated by dominantly using density functional theory to investigate their dependence of functionals. Since these systems have the property that the charge is from localization to delocalization, the optimized structures are sensitive to the functionals. The geometric optimizations show that CAM-B3LYP and omega B97X-D functionals are good choices for delocalized systems and LC-omega PBE and M06HF are suitable for the systems from charge almost localization to localization. The calculations of electronic couplings demonstrate that the pure functional generally underestimates the electronic couplings whereas the pure HF overestimates them. Furthermore, the electronic couplings from the conventional generalized Mulliken-Hush method are very sensitive to the HF component in functionals, which makes it a challenge to accurately estimate the values. A new reduced two-state method is thus proposed to overcome the deficiency, and the obtained electronic couplings are less sensitive to the omega value in LC-omega PBE functional and they are also consistent with the experimental data.