Photonic crystals with periodic nanostructures infiltrated by nematic liquid crystals were investigated based on Landau-de Gennes theory. We studied the fine structures of the system within different amplitudes on the sinusoidal boundaries. When modulating the amplitude, the location of the defects will change. Two new director profiles occurred, and the state observed in Appl. Phys. Lett.87, 241108 (2005)APPLAB0003-695110.1063/1.2139846 also appeared. The transmittance curves show a redshift of ${\sim} {0.1}\,\,\unicode{x00B5}{\rm m}$∼0.1µm in the mid-infrared spectra when increasing the amplitude. The location change of defect rings will induce a shift of ${\sim} 22.4\,\,{\rm nm}$∼22.4nm. Variations in sinusoidal boundaries will have an effect on the transmittance spectrum. Elastic anisotropic will also induce a small shift when the structure is fixed. Results could be useful in designing new types of photonic crystal devices or sensors.