Adsorbents based on carbonaceous materials, polymers, clays, and inorganic materials are common in the literature, but adsorbents designed from organic materials such as self-assembled heterocyclic compounds have not been studied so far. In this study, a new adsorbent pyrimidone derivative (DHPM) was synthesised employing a green protocol to tone down the cationic dye Methylene Blue (MB) from aqueous solution. The synthesised self-assembled bio-inspired molecules is characterized using Ultraviolet Spectroscopy (UV-Vis), Fourier transform infrared (FT-IR), 1H NMR & 13C NMR and Thermogravimetric analysis (TGA). The self-assembled molecule's propensity to adsorb MB dye was investigated as a function of MB concentration, time, temperature, pH and adsorbent dosage. The enhancement of adsorption capability over the cationic dye has been discussed in this script. A detailed examination of the adsorption kinetics revealed that the study conforms to pseudo-second-order model. Isothermal adsorption study over the MB dye were used with several models. Langmuir-Freundlich model was found to be the most accurate, with an adsorption capacity of 233.99 mg/g. The results are endothermic and spontaneous for the thermodynamic study of adsorption over MB dye onto the pyrimidone derivative.