Information of molecular orientation in nematic liquid crystal (LC) is attractive and important for applications in the field of display devices. We demonstrate a novel method using a birefringence scanning near-field optical microscope (Bi-SNOM) with a probe which is inserted into the LC thin film to detect the molecular orientation from its birefringence responses in the thickness direction of the LC thin film. The probe is laterally vibrated when going forward into the LC thin film, and the retardation and azimuth angle are recorded as the probe going down. Firstly, the thickness of the LC thin film is measured by the shear force detection. Since the shear force acts as a stimulation to reorientate the LC molecules above the substrate surface, we can detect the molecular orientation caused by a polyimide alignment substrate and the effect to molecular orientation caused by vibration of fibre probe. As a result, the orientation profiling of the LC film in depth direction is obtained in both the cases that the direction of probe vibrating is vertical/parallel to the rubbing direction of the alignment film.Furthermore, the thickness of completely orientated layers just above the substrate surface can also be obtained by either vibrating probe or no-vibrating probe. Ultimately, the LC thin film can be modelled in thickness direction from all the results using this method.