Nanoimprint lithography (NIL) was carried out on precursor of polyimide (PI), poly(amic acid) film, and then hard baking to obtain imprinted PI film. The molecular aggregation states of imprinted PI films before and after hard baking were investigated by grazing-incidence wide-angle X-ray diffraction comparing with the one of flat PI film. It was found that NIL and hard baking can strongly affect the molecular aggregation states of PI film. Before hard baking, PI chain is aligned parallel to the line direction on the line. After hard baking, the alignment in ordered domain was changed to that the PI molecule of which chain axis is perpendicular to the line direction is significantly increased, while, PI molecule of which chain axis is parallel to the line direction is decreased after hard baking. Through comparing with the flat PI, crystallinity of imprinted PI film has been significantly enhanced.