The invention discloses an atmospheric waveguide interference optimization method and system. According to the method and the system disclosed by the invention, interfered cells are sorted according to scene information; furthermore, an interference source is searched in a grading expansion manner, so that accurate locating on the interference source is realized; furthermore, priorities of the interfered cells are divided; according to the priorities, the various cells are adjusted in real time; simultaneously, real-time dynamic data acquisition is adopted; automatic optimization adjustment iscarried out by taking one hour as the optimization granularity; and thus, the interfered cells are effectively optimized in time. The atmospheric waveguide interference optimization method and systemdisclosed by the invention can be widely applied to the field of communication.