Traces of quaternary ammonium salt surfactant on its derived PA6/6.6 polymer nanocomposite were investigated by differential scanning calorimetry (DSC) and thermogravimetric analysis coupled with Fourier transform infrared spectroscopy (TGA-FTIR). PA6/6.6 polymer nanocomposite was produced via masterbatch extrusion process. Surfactant modified organoclay has an effect on both melting and crystallization at processing temperature. Melting of immiscible surfactant crystals at lower temperatures than room temperature could be of serious health concern especially when the polymer nanocomposite is intended for food packaging applications.