Betulin diacetate (BDA) has a variety of biological activities, but poor solubility in water limits its application. The use of arabinogalactan (AG) as a complexing agent is a promising method for solving the problem of solubilization of drugs. In this work, influence of microwave (MW) irradiation on the properties of AG and BDA and their interaction in the aqueous suspension with formation of a water-soluble supramolecular complex was studied. It is shown that the MW heating of AG under hard conditions can lead to degradation of the biopolymer. The use of MW heating allowed significantly reducing the complex preparation time compared to the conventional synthesis in a water bath. The preliminary mechanical treatment of the mixture of components, leading to the formation of mechanocomposites, inhibited the reaction between the components in the aqueous suspension under MW irradiation. The IR spectroscopy method has shown that a supramolecular complex formed under MW irradiation similar to that formed by conventional heating. BDA-AG complex was isolated from a MW heated solution as a thin film, which may be a promising material for pharmaceutical applications.