Uncertainties of the ground motions and structural parameters are the main factors that limit the accuracy of embankment seismic fragility assessment. In response to the uncertainties of the ground motions, artificial synthesizing method of the near-fault pulse-like ground motions was proposed, and 15 ground motions with the rupture fault distances ranging from 1 to 15 km were synthesized by taking the Chi-Chi earthquake in Taiwan, China, as an example. The Xi’an-Baoji expressway K1125 + 470 embankment was taken as the research object, and a total of 12 structural parameters were selected as the design variables, namely, the elastic modulus, bulk modulus, shear modulus, density, cohesion force, and internal friction angle of the embankment fill and soil foundation, respectively. In response to the uncertainties of these parameters, 3 principal components with large impacts on the embankment seismic fragility were extracted based on the principal component analysis. Mapping relationships among the principal components and embankment seismic damages were analyzed using the uniform design response surface method, and the seismic fragility assessment was carried out and the fragility curves were plotted. The research results are consistent with the actual embankment seismic damage conditions of the Chi-Chi earthquake, indicating that the proposed method is scientific and reasonable. It also shows that it would obviously overestimate the seismic performance in the embankment seismic fragility assessment without considering the uncertainties of the ground motions and structural parameters.