In the paper, two kinds of CdS nanorods with diameter of 50-150 nm were synthesized by using amphiphilic alanine as the templating reagent. XRD, TEM and polarized light microscopy were used to examine the course of CdS growth. The nanorod with a hexagonal pore microstructure was fabricated when the mesophase exhibited hexagonal morphology of the polarized light microscopy image. The XRD pattern of the nanorods with hexagonal pore microstructure showed a clear peak in 2θ=0.88° which suggested the existence of hexagonal pore. While the mesophase disappeared and isotropic polarized light microscopy image shows that CdS would propagate into nanorod without hexagonal pore. It was deduced that nanorods with hexagonal pore grow in the hole of hexagonal liquid crystal and those CdS growth without hexagonal pore are in isotropic solution by the absorption of amphilphilic alanine. It was suggested that different nanostructures could be generated under various chemical micro-environments to reveal their special functionalities.