In this work, a water-soluble supramolecular complex was synthesized in an aqueous suspension of betulin diacetate (BDA) and arabinogalactan (AG) upon microwave heating. Microwave heating allows reducing the time required for the complex formation, compared with conventional heating in a water bath. The specific effect of microwave irradiation on the initial reagents and preparation of a supramolecular complex was studied. In contrast to conventional heating, under microwave heating AG macromolecules may break into roughly equal fragments when the temperature increases up to 100 °C. A change in the surface morphology of BDA crystals under microwave heating of the suspension suggests that microwave irradiation facilitates the dissolution of BDA in water. It has been shown that the use of dimethylsulfoxide as a reaction medium for microwave heating led to a decrease in BDA content in the product due to the inclusion of DMSO into AG macromolecules. The BDA–AG complex was isolated from the microwave-heated aqueous solution, after water evaporation, as a thin amorphous film, which exhibited antitumor activity against Ehrlich ascites carcinoma cells and can be a promising material for pharmacological applications.