A series of branched waterborne polyurethane associative thickener (BHEUR) were prepared, polyethylene glycol (PEG) and isophorone diisocyanate(IPDI) as raw materials, and homemade branched type nuclear was introduced. The molecular structure of the obtained BHEUR was characterized by means of FTIR and GPC. The thickening property and the rheological property of BHEUR solution were studied by viscometer and rotational rheometer，considering the influences of different structures on the thickening effect of BHEUR. The results showed that when the molecular weight of PEG was 4000, the BHEUR-4 formed presented good self-thickening ability and thickening effect on PU emulsion. The viscosity of PU emulsion can be 50112mPa.s when the mass fraction of BHEUR-4 added was 1.6%. The test of rheological property showed that the four kinds of samples exhibited different degrees of shear-thinning behaviors with the increase of shear rates and such phenomenon of BHEUR-4 could occur under the lower shear rates, proving that it has formed a perfect associative network structure. The effect of BHEUR solution on the particle size of PU emulsion displayed that the synthetic BHEUR had good thixotropy.