Poly(trimethylene terephthalate) (PTT) nanocomposites with two different clays were fabricated via a novel two-step process. Structure, morphology, and cold crystallization of these nanocomposites were studied using differential scanning calorimetry (DSC), Fourier transform infrared (FTIR) spectroscopy, and X-ray diffraction (XRD). XRD results reveals that PTT-15A. nanocomposites were fully exfoliated, whereas PTT-30B nanocomposites were partially exfoliated. Non-isothermal cold crystallization temperature and the crystallinity of non-isothermally cold-crystallized PTT-15A nanocomposites increased with increasing 15A content. The crystallinity of isothermally cold-crystallized PTT-15A nanocomposites was shown to increase with crystallization temperature and the clay content, but no clear trend in crystallinity was observed for PTT-30B nanocomposites. The combination of FTIR and DSC has been used to determine the conformational changes during isothermal cold crystallization. The results show that the crystalline gauche and amorphous gauche conformations increased and the amorphous trans conformation decreased with crystallization temperature and clay content for PTT-15A nanocomposites, whereas no trend was observed for PTT-30B nanocomposites.