Internal-external coupled full-scale modeling for a rectangular-to-elliptical shapetransition (REST) scramjet under a high flight Mach number of 12 was modeled by Improved Delayed Improved Delayed Detached Eddy Simulation (IDDES) and a Dynamic Zone Flamelet combustion Model (DZFM). The modeling is based on a total cell number of 63.03 million and a 13s/33r nonequilibrium hydrogen mechanism. The effect of differential diffusion was investigated for the flow fields, efficiency indices, and thrust performance. A sensitivity analysis of the zone discretion was conducted to select the optimal zone number with acceptable accuracy yet high efficiency. The predicted wall pressure is comparable with the measurements. Detailed analysis of the characteristics of hypersonic flow, reacting species, and combustion was analyzed by using Takeno Flame Index (TFI) and Chemical Explosives Mode Analysis (CEMA), etc.