Hypersonic flow over a canonical 25°−55° double-cone configuration with a freestream Mach number of 10.38 is numerically investigated. In contrast to a relatively stable and moderate separation region in experiments, axisymmetric calculations in the literature demonstrated that the separation bubble continuously grew and notably exceeded the experimental result. To explain the causes of the discrepancy, time-accurate axisymmetric and Three-Dimensional (3D) simulations are conducted for the double-cone flow to investigate the evolution of three-dimensionality and unsteadiness. Both the axisymmetric calculation and the 3D simulation without external disturbances predict a significantly larger separation region than that in experiments and misrepresent the distributions of surface pressure and heat flux. The random forcing approach with two levels of noise amplitude is then applied to 3D simulations. A better agreement with the measured data is observed for the time-averaged heat flux and pressure when the white noise is enforced. As the forcing amplitude is increased, the agreement is slightly improved. However, discrepancies between the 3D results and experimental data still exist in the prediction of the heat flux and pressure distributions, indicating the essential difference between the injected white noise and the wind tunnel freestream disturbances. Realistic noise models are required to reveal the sources of such discrepancies.