The study of the structure of matter is one of the main tasks of chemistry. The problem can be solved with the help of graph theory, which allowed us to find an unexpected way to solve our logical problem. Thus, the aim of our article was to master the theory of graphs for constructing the structural formulas of organic compounds. Prediction of chemical reactions, the possibility of systematization and study of the essence of basic chemical concepts, such as structure, configuration of atoms and molecules, confirmation, isomerism, and, undoubtedly, the quantum-mechanical basis of the interaction of molecules, all this is possible using chemical graphs. Graph theory allows a non-standard way to approach the problem of constructing the structural formulas of molecules of organic compounds.