Selective Laser Sintering (SLS) is one of the most mature and engineered polymeric 3D printing technologies, and the produced part is characterized by homogeneous polymorphism, which make the sintered material possess an ordered crystalline phase distribution and thus present a self-formed composite structure. This is due in large part to the special processing method during the SLS process. However, molecular motion mechanism between different phases remain unclear and further exploration is needed. Therefore, this paper firstly investigates the molecular motion mechanism concerning special composite phase structure of SLS-processed PA6 based on 2D correlation fourier transform mid-infrared (FT-MIR) spectra. The results show that although the crystal structure of the LT-alpha phase is less-ordered, the groups in LT-alpha change later than those in HT-alpha as the temperature increases. The overall movement sequence is: HT-alpha( >) interphase (>) LT-alpha, and the motion mode in the individual phase is the skeleton movement of carbon chains driven by H-bonds whereas the movement of interphase H-bonds is driven by the synergistic effect of the chain in HT-alpha. Besides, the symmetric methylene (v(s) (CH2)) vibrates firstly both for HT-alpha and LT-alpha, and then is the stretching vibration of asymmetric methylene (v(as) (CH2)).