Multiscale nonequilibrium physics at large variations of local Knudsen number are encountered in applications of aerospace engineering and micro-electro-mechanical systems, such as high-speed flying vehicles and low pressure of the encapsulation. An accurate description of flow physics in all flow regimes within a single computation requires a genuinely multiscale method. The adaptive unified gas-kinetic scheme (AUGKS) is developed for such multiscale flow simulation. The AUGKS applies discretized velocity space to accurately capture the non-equilibrium physics in the multiscale UGKS, and adaptively employs continuous distribution functions following Chapman–Enskog expansion to efficiently recover near-equilibrium flow region in GKS. The UGKS and GKS are dynamically connected at the cell interface through the fluxes from the discretized and continuous gas distribution functions, which avoids any buffer zone between them. In this study, the AUGKS with rotation and vibration non-equilibrium is developed based on a multiple temperature relaxation model. The real gas effect in different flow regimes has been properly captured. To capture aerodynamic heating accurately, the heat flux modifications from the rotation and vibration modes are also included in the current scheme. Unstructured discrete particle velocity space is adopted to further improve the computational performance of the AUGKS. Numerical tests, including Sod tube, normal shock structure, high-speed flow around the two-dimensional cylinder and three-dimensional sphere and space vehicles, and an unsteady nozzle plume flow from the continuum flow to the background vacuum, have been conducted to validate the current scheme. In comparison with the original UGKS, the current scheme speeds up the computation, reduces the memory requirement, and maintains the equivalent accuracy for multiscale flow simulation, which provides an effective tool for nonequilibrium flow simulations, especially for the flows at low and medium speed.