The main operational characteristics of polyamide-6-montmorillonite (PA6/MMT) nanocomposites, which determine their fields of application, mainly depend on the crystal structure and crystallinity of the polymer. Therefore, the study of the crystalline behavior of PA6 in such nanocomposites is of considerable scientific and practical importance. In this work, the structure, crystalline, and thermal properties of nanocomposites based on PA6 and modified MMT prepared in a formic acid solution were investigated using the methods of differential scanning calorimetry (DSC) and X-ray Diffraction (XRD). It was established that during the manufacture of PA6/MMT nanocomposites in a solution, the dominant crystal structures are the thermodynamically stable α structures of PA6. The crystallinity degree of PA6 in nanocomposites is about 1.5 times higher than that of the original PA6. It is shown that after additional thermomechanical treatment of nanocomposites on a capillary viscometer at 230°С and a load of 5 kg, the uniformity of the distribution of exfoliated MMT in the polymer matrix increases, as a result of which the crystalline structure of PA6 changes and its glass transition and melting temperatures increase. These changes in the PA6 structure also have a significant impact on the melt flow index and the softening temperature of nanocomposites.