The changes in the structural organization of a polymeric matrix of humic substances contained in therapeutic mud, coal and shale which take place in the process of their alkaline hydrolysis have been studied. These humic substances were isolated from some of the Mongolian deposits. Cumulative evidence on the composition and structural organization of humic substances provides a necessary base for creating new humic substances and medicines with enhanced levels of biological activity. The composition of ashy elements in initial and hydrolyzed humic substances of various types has been analyzed, and the results indicate that aluminosilicate present in the matrices belongs to sheet minerals and is identified by X-ray analysis as illite. The functional composition of humic substances has been thoroughly examined by IR and electronic spectroscopy. It is shown that during alkaline hydrolysis, the oxidation level of all samples increases by 15–25 %, and their water solubility exhibits multifold enhancement. Chromaticity coefficients of humic substances isolated from mud and coals increase more significantly after oxidative hydrolysis than those of shales. Functional groups of humic substances are freed from mineral components and become ionized in the alkaline medium. The morphology study of humic substances contained in medical mud, coal and shale has shown that they feature a layer structure with an uneven packing type of. It is noted that in the course of alkaline hydrolysis the morphology of the objects under study demonstrates a homotypic change towards a looser structure caused by reconfiguration of macromolecules. Varied effects of alkaline hydrolysis on the molecular structure of humic substances contained in therapeutic mud, coal and shale from Mongolian natural sources increases their reactivity.Keywords: humic substances, therapeutic mud, coal, shale, structure, morphology, alkaline hydrolysis.