The enrichment of the molecular structure of silk fibroin by selenium atom led to an increase in the branching of fibroin macromolecule. As a result, the amorphous fraction of fibroin microfiber increases which leads to an increase in the strength characteristic of the silk thread. At the same time, this change in the supramolecular structure of fibroin involving a selenium atom has enabled us to study the two-modification mechanism for crystallizing fibroin microfibers. Based on studies on the use of temperature-gravimetric and X-ray diffraction (XRD) analysis and relative changes in the proportion of amorphous and crystalline regions, we came to the conclusion that fibroin microfibrils consist mainly of extended crystallites CSC – crystallites with the stretched chains. They alternate along the axis of microfiber with amorphous layers, the sizes of which are smaller than the sizes of the folded crystallites (CFC). Therefore, CFC cannot be located in amorphous layers between the CSC along the microfiber’s axis. As a result, the ability to fold branched sections of the macromolecule decreases, that is, CFC decreases. This increases the proportion of amorphous areas of microfibers of the fibroin. In the model, which is proposed by author non-crystallized in the form of CSC, segments of a macromolecule, on the sides of the central core and attached to it, restored their crystal structure (CFC) – with folded conformation of chains.