Mesoporous silica thin films with aligned mesochannels in one direction at large scales will be applied in optics, electronics, separation technologies etc. We propose herein a new photo-aligning and micro-patterning technique for mesochannels of a silica thin film using a photo-crosslinkable polymer liquid crystal (PPLC) film. The PPLC film was uniaxially oriented by exposure to linearly polarized UV (LPUV) light and annealed at a liquid crystal phase temperature. On the PPLC film, a mesoporous silica thin film was prepared. The orientation of the mesochannels was evaluated by in-plane XRD measurements. It was confirmed that the mesochannels was aligned parallel to the polarized direction of the irradiated LPUV light.