This paper develops a three-dimensional (3D) thermal-structure coupling model, implements transient stress analysis of thermoelastic contact of disk brakes with a frictional heat variation and identifies the source of the thermal fatigue. This thermostructure model allows the analysis of the effects of the moving heat source (the pad) with a variable speed and integrates the heat flux coupling between the sliding surfaces. To obtain the transient stress/temperature fields of the brake under an emergency braking, the thermoelastic problem under this 3D model is solved by the finite element method. The numerical results from the analysis and simulation show the temperature/stress of the disk presenting periodic sharp fluctuation due to the continuous cyclic loading; its varying frequency corresponds to the rotated cycle times of the braking disk. The results demonstrate that the maximum surface equivalent stress may exceed the material yield strength during an emergency braking, which may cause a plastic damage accumulation in a brake disk, while a residual tensile hoop stress is incurred on cooling. These results are validated by experimental observation results available in the literature. Based on these numerical results, some suggestions for avoiding fatigue fracture propagation are further presented.