The generation of pretilt angles for nematic liquid crystal aligned rubbed polyimide on the rubbed polyimide surface containing tri fluoromethyl moieties has been investigated. The characters of the rubbed polyimide films were studied by using X-ray photoelectron spectroscopy(XPS) and atomic force microscopy(AFM). The uneven distribution extent of fluorine content along the depth of the polyimide films could be reduced by rubbing, thus the interaction between liquid crystal molecules and polyimide molecules decreased. It is also showed that the aggregation state of polyimide molecules was changed and polyimide chains aligned along the rubbing direction, so the orientation direction of the liquid crystal molecules was the same as the rubbing direction. The orientation effect of the liquid crystal molecules on the rubbed polyimide surface can be attributed to the combined effects of the Van der Waals dispersion interaction between and polyimide and liquid crystal molecules, and the alignment of the orientation direction of polyimide chains with the rubbing direction.