A series of hyperbranched waterborne polyurethanes (HWPU-4, HWPU-6 and HWPU-12) containing hydrophobic end groups were prepared by the hyperbranched core and the polyurethane prepolymer. The core was polyol including pentaerythritol (PE-4), hyperbranched polyester with six hydroxyl end groups (HPE-6) and hyperbranched polyester with 12 hydroxyl end groups (HPE-12). The polyurethane prepolymer was synthesized by hexamethylene diisocyanate (HDI), polyethylene glycol (PEG) and hexadecanol. The structures of the hyperbranched cores and HWPUs were characterized by Fourier transform infrared spectra (FTIR), nuclear magnetic resonance spectra (1H NMR and 13C NMR) and gel permeation chromatography (GPC). The influences of HWPU content and structure on its thickening property were studied by the measurement of rotary viscosity. The results showed that the thickening effect of HWPU enhanced with the increase of HWPU content in the aqueous polyurethane emulsion. The thickening effect of HWPU-6 was superior to that of HWPU-4 and HWPU-12 with the same length of hydrophilic chain. In addition, the thickening effect of HWPU with the same core was related to the length of hydrophilic chain and the relative content of hydrophobic end groups.