In this paper, an advanced statistical physics adsorption model (double-layer model with two energies) is successfully established. On the basis of this model, statistical thermodynamic functions (e.g., entropy (S), Gibbs free enthalpy (G), and internal energy (Eint)), pore size distribution (PSD), and site energy distribution (SED) functions were successfully developed and applied to investigate the adsorption mechanisms of nanopore-structured ashitaba waste-based activated carbons (AWAC) and walnut shell-based activated carbons (WSAC) on Congo red (CR) and methylene blue (MB) dyes in aqueous solutions. Statistical thermodynamic results indicated that the adsorption reactions involved in this study are entropy-increasing, endothermic, and spontaneous in nature. Furthermore, PSD and SED described the heterogeneity of these adsorbents in terms of geometry or structure and energy and illustrated that the aforementioned adsorption processes are endothermic physisorption. All in all, this study contributed to broadening the understanding of the adsorption mechanisms of dye molecules onto biomass-based activated carbons.