We deal with non-hydrostatic mesoscale atmospheric modeling using the fully implicit space-time discontinuous Galerkin method in combination with the anisotropic hp-mesh adaptation technique. The time discontinuous approximation allows the treatment of different meshes at different time levels in a natural way which can significantly reduce the number of degrees of freedom. The presented approach generates a sequence of triangular meshes consisting of possible anisotropic elements and varying polynomial approximation degrees such that the interpolation error is below the given tolerance and the number of degrees of freedom at each time step is minimal. We describe the discretization of the problem together with several implementation issues related to the treatment of boundary conditions, algebraic solver and adaptive choice of the size of the time steps. The computational performance of the proposed method is demonstrated on several benchmark problems.