A zonal nonequilibrium model (ZNM) based on the concept of zonal representation of the nonequilibrium relaxation times is proposed. ZNM, together with dynamic zone flamelet model, zonal dynamic adaptive chemistry, and zonal in situ adaptive tabulation, forms the complete framework for nonequilibrium combustion modeling. The framework is then applied to the modeling of a high-Ma scramjet operating at Mach 12 based on improved delayed detached eddy simulation with a total of 92.52 million cells. The nonequilibrium effects exerted noticeable influences on the flow characteristics and engine performance through two main mechanisms, i.e., cooling and radical farming. Under a reduced flame temperature, the mixing efficiency increases due to the lower viscosity, whereas both the combustion efficiency and thrust recede. The Borghi diagram incorporating the compressibility effect shows that nearly 2/3 of the zones are in the flamelet mode, and the flamelet mode distributes wider under nonequilibrium.