To solve the problems of storage stability and the volatile organic compound emission of waste-rubber-powder-modified bitumen, the strategy of preparing composite modifiers using waterborne polyurethane coating for waste rubber powder was proposed in an early-stage work. However, the effect of polyurethane/waste rubber powder composite modifier on the performance of asphalt mixture is unclear, which limits the further popularization of this technology. Therefore, this work mainly investigates the characteristics of composite modifiers and their influence on asphalt mixture. The results indicate that the optimum ratio of polyurethane to waste rubber powder is about 1:1, which can give the composite modifier sufficient mechanical properties and acceptable economic benefits. The scanning electron microscopy images also confirm that polyurethane can densely encapsulate waste rubber powder. The physical properties experiment of bitumen shows that composite modifiers can increase the softening point and viscosity of bitumen but reduce the ductility and penetration of bitumen. Moreover, it was also found that composite modifiers can significantly improve asphalt mixtures’ resistance to permanent deformation and moisture damage. This can be attributed to the increase in the consistency of the asphalt binder due to the composite modifier. However, the anti-cracking properties of asphalt mixtures will be destroyed if the content of the composite modifier is too high. Therefore, it is necessary to balance the high and low temperature properties of asphalt mixtures when determining the dosage of composite modifiers in practical engineering. The results of this paper can provide a reference for the green application of waste-rubber-powder-modified bitumen.