A new version of NCAR Whole Atmosphere Community Climate Model with thermosphere/ionosphere extension (WACCM-X) has been developed. The main feature of this version is the species-dependent spectral element (SE) dynamical core, adapted from the standard version for the Community Atmosphere Model (CAM). The SE is on a quasi-uniform cubed sphere grid, eliminating the polar singularity and thus enabling simulations at high-resolutions. Molecular viscosity and diffusion in the horizontal direction are also included. The Conservative Semi-Lagrangian Multi-Tracer Transport Scheme (CSLAM) is employed for the species transport. An efficient regridding scheme based on the Earth System Modeling Framework (ESMF) is used to map fields between the physics mesh and geomagnetic grid. Simulations have been performed at coarse (~200 km and 0.25 scale height) and high (~25 km and 0.1 scale height) resolutions. The spatial distribution of the resolved gravity waves from the high-resolution simulations compare well with available observations in the middle and upper atmosphere. The forcing by the resolved gravity waves improves the wind climatology in the mesosphere and lower thermosphere in comparison to the coarse resolution simulations with parameterized forcing. It also impacts the thermospheric circulation and compositional structures, as well as thermospheric variablity. While larger scale waves are dominant energetically at most latitudes, smaller scale waves contribute significantly to the total momentum flux, especially at mid-high latitudes. The waves in the thermosphere are shown to be strongly modulated by the large-scale wind through Doppler shift and molecular damping, and they cause large neutral atmosphere and plasma perturbations.