In this work, using photoacoustic Fourier transform infrared spectroscopy (FTIR) we have studied the structural distortion of clay crystal structure in organically modified montmorillonite (OMMT) and polymer clay nanocomposites (PCN). To study the effect of organic modifiers on the distortion of crystal structure of clay, we have synthesized OMMTs and PCNs containing same polymer and clay but with three different organic modifiers (12-aminolauric acid, n-dodecylamine, and 1,12-diaminododecane), and conducted the FTIR study on these PCNs. Our previous molecular dynamics (MD) study on these PCNs reveals that significant nonbonded interactions (van der Waals, electrostatic interactions) exist between the different constituents (polymer, organic modifier, and clay) of nanocomposites. Previous work based on X-ray diffraction (XRD) and differential scanning calorimetry (DSC) on the same set of PCNs shows that crystallinity of polymer in PCNs have changed significantly in comparison to those in pristine polymer; and, the nonbonded interactions between different constituents of PCN are responsible for the change in crystal structure of polymer in PCN. In this work to evaluate the structural distortion of crystal structure of clay in OMMTs and PCNs, the positions of bands corresponding to different modes of vibration of Si-O bonds are determined from the deconvolution of broad Si-O bands in OMMTs and PCNs obtained from FTIR spectra. Intensity and area under the Si-O bands are indicative of orientation of clay crystal structures in OMMTs and PCNs. Significant changes in the Si-O bands are observed from each vibration mode in OMMTs and PCNs containing three different organic modifiers indicating that organic modifiers influence the structural orientation of silica tetrahedra in OMMTs and PCNs. Deconvolution of Si-O bands in OMMTs indicate a band at approximately 1200 cm(-1) that is orientation-dependent Si-O band. The specific changes in intensity and area under this band for OMMTs with three different organic modifiers further confirm the change in structural orientation of silica tetrahedra of OMMTs by organic modifiers. Thus, from our work it is evident that organic modifiers have significant influence on the structure of polymer and clay in PCNs. It appears that in nanocomposites, in addition to strong interactions at interfaces between constituents, the structure of different phases (clay and polymer) of PCN are also altered, which does not occur in conventional composite materials. Thus, the mechanisms governing composite action in nanocomposites are quite different from that of conventional macro composites.