A packaging method and a packaging structure of a film bulk acoustic resonator are provided. The packaging method includes: providing a resonant cavity main structure including a first substrate and a film bulk acoustic resonant structure having a first cavity formed therebetween; forming a resonator cover by providing a second substrate and forming an elastic bonding material layer containing a second cavity and an initial opening; bonding the resonant cavity main structure and the resonator cover together through the elastic bonding material layer and removing elasticity of the elastic bonding material layer, where the second cavity is at least partially aligned with the first cavity; forming a through-hole containing the initial opening and a hole connected with the initial opening and passing through the resonator cover; and forming a conductive interconnection layer covering a sidewall of the through-hole and a portion of a surface of the resonator cover.