The invention discloses waterborne polyurethane and a preparation intermediate and a preparation method thereof. The preparation method of the waterborne polyurethane comprises the following steps: S1, preparing an intermediate which has a structure as shown in formula I; S2, under the condition of prepolymerization reaction, promoting the intermediate to be in contact reaction with polyol, firstpolyisocyanates and organic carboxylic acid to form prepolymer, wherein the number-average molecular weight of the organic carboxylic acid is smaller than 250 g/mol, and the organic carboxylic acid contains two hydroxyls; and S3, carrying out emulsification treatment on the prepolymer under the condition of emulsification, and carrying out chain extension treatment on the prepolymer subjected to emulsification treatment. According to the method, the intermediate which has the structure as shown in formula I is added in a process of prepolymerization reaction, a prepolymer which has relativelylow viscosity can be prepared, an organic solvent is not required, but the waterborne polyurethane with high solid content can be prepared by emulsification.