Among transition metal oxides, manganese dioxide nanostructures are proven to be green in chemistry, highly active, economical and durable. The main focus of this research paper is on adsorption isotherms and removal of methylene blue (MB) from aqueous solutions by MnO2 nanorods. MnO2 nanorods were fabricated by using hydrothermal method and characterized by EDX, SEM, BET, FTIR, XRD, XPS and zeta potential. Through performing experiments of the liquid phase adsorption, studied the effects of preliminary parameters, like contact time, initial concentration, adsorbent dosage, temperature and solution pH. The optimum operating parameters of MB removal by MnO2 were obtained to be 0.04 g catalyst dosage, 10 mg/L MB concentration, and 288 K temperature. To characterize and express the equilibrium isotherms, collected equilibrium data numerically modeled by using different models such as Temkin, Freundlich, and Langmuir. High values of correlation coefficients (0.8421) illustrated that the Langmuir isotherm model was the best fit for collected experimental data. The model data exhibited that the adsorption kinetics follow the pseudo-second-order kinetics model. The thermodynamic data were also explored and explained. The obtained negative ΔG° implied the spontaneous quality of adsorption and the negative ΔS° (−0.12 kJ/mol·K) indicated that the MB is adsorbed with lower randomness on MnO2 surface. Furthermore, a classical all-atom molecular dynamic (MD) simulation was used to study the adsorption properties of MB solutions on MnO2 surface. To this end, aqueous solutions containing various concentrations of MB were confined between two surfaces of MnO2. The distribution of each component of the solution at the vicinity of MnO2 surface was analyzed. MD simulations confirmed the adsorption of MB molecules on the MnO2 surface. The adsorption capacity represented different changes due to variation of concentration and temperature. As the temperature rises from 288 to 318 K, it resulted in decreasing of adsorption capacity and increasing of the diffusion coefficient. As concentration increases from 10 ppm to 35 ppm, the adsorption capacity enhanced while the diffusion coefficient decreased. The present study improves our understanding on the removal of organic pollutants from aqueous solutions utilizing MnO2 nanomaterials and reveals the mechanism of the uptake of MB on this material. To our knowledge, the structural and dynamic properties of MB solutions on MnO2 as an adsorbent through MD simulations have not been investigated to date.