We present a struture-preserving solver for particle-wave interaction in magnetized plasmas. The solver combines a conservative local discontinuous Galerkin (LDG) scheme for the interaction part with a trajectory averaging method for the Hamiltonian flow part. The proposed LDG scheme is an extension of the conservative scheme we developed in 2023. The trajectory averaging method significantly reduces computational cost by taking advantage of the multiscale feature of this system. By introducing a novel concept “trajectory bundle”, we transform a continuous topological problem into a discrete graph theory problem. Numerical examples for a non-uniform magnetized plasma in an infinitely long symmetric cylinder is presented. It is verified that the connection-proportion algorithm allows to distinguish different trajectory bundles, and the proposed DG scheme rigorously preserves all the conservation laws.