The invention discloses a functional paper reparation method and application thereof. The method comprises two steps: 1, connecting a double-bond functional group on the surface of the paper under theaction of double-bond silane; 2, functionalizing the paper with the double-bond functional group connected on the surface by utilizing the mercaptan-olefin click chemical reaction under the action ofmercaptan with different functional groups, and obtaining the different functionalized paper. Meanwhile, the mercaptan-olefin click chemical reaction is triggered by ultraviolet light, a photomask isintroduced in an illumination process to realize patterning of the functional paper, the controllability is very good, and the resolution ratio is relatively high. The disclosed method can achieve functionalization and patterning of different types of paper in different sizes within minutes, the preparation process is simple, fast and controllable, the preparation method is very strong in universality and can produce on a large scale, and the prepared functionalized paper can be applied to the fields of hydrophobic substrates, paper chips, cell culture, etc.