According to the advent of ubiquitous world, the requirement for the mobile information devices with high display quality and compact device size is surprisingly increased. Among the diverse candidates for this mobile display system for mobile devices, Liquid Crystal on Silicon (LCoS) is the most competitive device due to the high aperture ratio and simple fabrication process. The inorganic liquid crystal (LC) alignment layers are widely used for LCoS devices because of the thermal and photochemical stability. In this work, the reactive sputtering was selected for the preparation method of inorganic LC alignment layers. The nitrogen (N-2) gas had the effect on the deposition process of SiO2 and the surface morphology of SiO2 thin layers were affected by the N-2 mixing ratio of sputtering gas. In addition, the LC alignment properties on SiO2 thin layer were also closely related with the N-2 mixing ratio and other sputtering conditions. In the case of high RF power of reactive sputtering, the N-2 mixing ratio has little effect on the LC alignment on SiO2 thin layers. However, in the case of low RF power of reactive sputtering, the LC alignment properties were enfeebled by increasing the N-2 mixing ratio. This result might be attributed to the change of the surface morphology of inorganic SiO2 thin layers.