Three different macromolecular diols were synthesized by the reaction of Poly(1,4-butanediol adipate) diol (PBA) and diisocyanate (Isophorone diisocyanate (IPDI), Hexamethylene diisocyanate (HDI) and Methylene-bis(4-cyclohexylisocyanate)(HMDI)) at the ratio of 2:1. Based on these macromolecular diols, waterborne polyurethane (WPU) adhesives were prepared. The structure and molecular weights of the WPU were characterized by Nuclear magnetic resonance spectroscopy (H-1 NMR), Fourier Transform Infrared Spectroscopy (FTIR) and Gel permeation chromatography (GPC) respectively. Furthermore, the hydrogen bonding interaction of WPU were analyzed by the deconvolution FTIR spectra. The results showed that the hydrogen bonded NH was increased when carbamate was in the soft segment. The crystallinity of WPU was tested by X-ray diffraction (XRD) and Differential scanning calorimetry (DSC). The results showed that the crystallinity of WPU2 (HDI) and WPU3 (HMDI) were enhanced, especially for WPU2. Meanwhile, the Tg,s as well as the mechanical strength, storage modulus, the contact angle and thermo-stability were increased with the introduced carbamate into soft segment. The T-peel tests of plasticized PVC/WPU/plasticized PVC joints and lap-shear tests of wood/WPU adhesive/wood joints were carried out. The results indicated that the carbamate in the soft segment could significantly enhance the adhesion of WPU at an appropriate activation temperature.