The paper presents the results of applying a new method, previously developed by the authors, based on precalculated sets of 3D distributions of a matter density. The method is designed to recognize the spatial 3D distributions of the synthesized intermetallic compounds in the volume of a nanoparticle. A set of 3D distributions of a matter density in the volume of a cubic Ti@Al core — shell nanoparticle corresponds to a set of successive time points. It is calculated based on the results of the computer molecular dynamics simulation of self-propagating high temperature synthesis in the nanoparticle. Computational experiments are performed using the LAMMPS software package. Based on the obtained results, thermal and microstructural analyses are performed, confirming the multistage mechanism for the formation of intermetallic phases during the SHS reaction in the Ti-Al reaction medium. The sets of 3D distributions of the matter density and 3D distributions of synthesized intermetallic compounds in the volume of a nanoparticle corresponding to the sequence of time points are calculated. The paper shows the advantage of the method for recognizing 3D distributions of synthesized intermetallic compounds, proposed by the authors, over the methods of similar analysis built into the OVITO software package.