The invention discloses a cationic waterborne polyurethane emulsion as well as a preparation method and application thereof, and belongs to the technical field of papermaking. According to the invention, toluene-2, 4-diisocyanate (TDI) is used as a main reaction raw material, polyethylene glycol (PEG-200, 400, 600 or 800) is used as a soft segment, tetrahydrofuran (THF) is used as a solvent, and 2, 4, 6-tri (dimethylaminomethyl) phenol is used as an end-capping reagent, and because the 2, 4, 6-tri (dimethylaminomethyl) phenol carries positive charges in an aqueous solution, the prepared waterborne polyurethane emulsion also carries positive charges, and under the action of charge attraction, the waterborne polyurethane emulsion can be well retained on negatively charged paper fibers. Besides, the cationic waterborne polyurethane emulsion prepared by the invention can be used as a papermaking wet end additive, obviously enhances the paper effect (the dry and wet strength, the tearability and the folding strength, especially the wet strength are obviously improved), and has a certain sizing effect. Moreover, the auxiliary agent can also be used for coating the surface of paper, so that the surface strength of the paper is improved, and even the surface porosity is adjusted.