On 17 June 2019, an M6.0 earthquake occurred in Changning County, Sichuan Province, China. Considerable highway subgrades were damaged in this earthquake. By investigating seismic damage of these subgrades, a systematical analysis of influence factors and failure mode of the damages on highway subgrade have been given. There is a close relationship between the damaged degree of subgrade and the distance of epicenter, fault distance, and structure type of subgrade. The seismic hazard investigation shows that the seismic damage of the cut-and-fill subgrade was more severe than that of the fill subgrade. Taking the Changning earthquake ground motion record as input, 3D dynamic finite element analyses were performed. The seismic damage mechanisms of cut-and-fill subgrade and fill subgrade were revealed. The numerical simulation confirmed that the cut-and-fill subgrade was more easily damaged by earthquakes compared with the fill subgrade. The fill-and-cut interface of the cut-and-fill subgrade had a notable plastic strain band after the earthquake, and the permanent displacement of the slope top was significant. In this manner, the numerical results are consistent with seismic investigation data. Considering the seismic investigation data for highway subgrades are rare, this paper may provide effective references for aseismic design and deformation control of highway subgrades.