Starch-based polymer systems have attracted a great deal of interest as a potential alternative to conventional plastics for packaging applications. Mechanical and thermal properties of these systems strongly depend on their local structure and molecular dynamics. In this study, the effects of urea and glycerol mixtures on structure and molecular mobility in thermoplastic starch/montmorillonite-type nanofiller composites were investigated using X-ray diffraction and nuclear magnetic resonance spectroscopy (²⁷Al, ¹³C, and ¹H). The X-ray diffraction patterns indicate intercalation of plasticizer molecules and starch chains inside the montmorillonite particles in all composites. The urea crystallites in most urea-containing composites and starch retrogradation in all composites with glycerol-plasticized starch were also deduced from X-ray diffractions. Changes in the ²⁷Al NMR spectra measured on the studied samples were related to the amount of plasticizer molecules available for interaction with exfoliated and reassembled MMT platelets. The ¹H NMR spectra shapes indicate that increased glycerol content results in greater molecular mobility, which causes starch retrogradation during sample ageing, inferred from T₁(¹³C) spin–lattice relaxation times and the change in C1 resonance shape in the ¹³C NMR spectra respectively. Starch retrogradation was not detected in the composites with urea-plasticized starch due to their rigid structure reflected in relatively long T₁(¹³C) spin–lattice relaxation times.