An approach to simulate thermal destruction processes of energetic materials has been developed. It is based on the classification of structural features for nitro compounds and the experimental data regarding their decomposition mechanisms. This approach consists of the mathematical simulation of thermal decomposition mechanisms to predict the likely reactions that may occur during the destruction of organic compounds. On the basis of contemporary experimental data on the decomposition of energetic materials from various chemical classes, a set of semi-empirical rules for modeling possible reaction pathways has been formulated. These rules allow the generation of a whole set of possible decomposition mechanisms for substances at different steps of their destruction. In this study, the suggested methodology is applied to 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) and hydrazine and to their binary energetic mixture. It has been shown that thermal decomposition of the binary system consists in decompositions of the separate compounds at the initial stage with subsequent collisions and interactions of the resultant intermediates and decomposition products at different stages. In addition to some experimentally found decomposition products, our simulation showed some other possible compounds among the final products.