Cow dung waste has caused severe environmental pollution and public health issues in China. In this study, the cow dung residues were used as a cheap renewable fiber to modify asphalt binder, providing a new solution for the proper disposal of cow dung waste. Three cow dung fibers with two lengths were prepared using different treatments, including original cow dung fiber (CDF), surface treatments of cow dung fiber (STCDF) and alkali treatments of cow dung fiber (ATCDF). The physicochemical properties of CDF, STCDF and ATCDF were analyzed by scanning electron microscope (SEM) and thermogravimetry (TG). The viscidity, rheological properties and fatigue characteristics of CDF modified asphalt binders (CDFMA) were evaluated using Brookfield viscometer and dynamic shear rheometer. The results showed that the rough surfaces of STCDF and ATCDF improved their thermal stability. STCDF and ATCDF enhanced the resistance to permanent deformation under high temperature conditions of modified asphalt binder. STCDF modified asphalt binders exhibited the best viscosity and rheological performance. The increase of fiber length was positively correlated with the high temperature deformation resistance of CDFMA. CDF, STCDF and ATCDF inhibited fatigue cracking of modified asphalt binders compared to base asphalt binders. ATCDF modified asphalt binders exhibited higher fatigue life and smaller crack under the same cyclic loading. The increase in fiber length had a slight improvement on the fatigue resistance of modified asphalt binders.