Isothermal crystallization of the nanocomposites based on aliphatic copolyamide (CoPA) containing bentonite (Bin), activated (K10) or organic modified montmorillonite (I30 P) clay were investigated using Differential Scanning Calorimetry (DSC) analysis. Results from the dynamic crystallization process denoted an improvement of the nucleation process, induced rather by K10 or 130 P clays than Btn clay. The data from isothermal crystallization were used to confirm a further reduction of kinetics and general crystallization rate in the CoPA matrix loaded with K10 and 130 P clays, despite already reduced crystallization kinetics of neat CoPA or loaded with Btn. It was proposed a two-dimensional growth mechanism of CoPA crystals induced by K10 and 130 P clays that was compared with a one-dimensional growth present in neat CoPA or filled with Btn clay. Small Angle X-Ray Scattering (SAXS) analysis of the isothermal crystallized samples had confirmed the morphology development and long period distribution in CoPA matrix. Furthermore, the SAXS results sustained a slight decrease in the clustering effect in the vicinity of clay interface. Consequently, the confinement effect induced by K10 and 130 P clays slowly increased the exfoliation level in these nanocomposites.