N-hexadecylated poly(p-phenylene terephthamide) (PPTA) comb-like polymers (PPTAC16), which are composed of PPTA backbone and hexadecyl side chains, were prepared by method of N-alkylation reaction. The molecular structure and thermal transition behavior of PPTAC16 were characterized by a combination of differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopy (FT-IR) technique. DSC results indicated that the crystallization of hexadecyl side chains, and the side chain crystallization is less perfect than that of n-hexadecane crystal. IR results showed that the ordered degree of the packing of CH2 group in the side chain crystallization is lower than that of n-hexadecane crystal. Variable temperature IR spectroscopic results revealed that the stretching vibration and bending vibration bands of methylene group experience an abrupt change with increasing of temperature which indicate the melting of the side chain crystallization, furthermore the main chain of PPTAC16 was found to undergo an irreversible change accompanying the melting of the alkyl side chain crystallization. And the molten state of CH2 group in the hexadecyl of PPTAC16 is different from that of liquid n-hexadecane.