The invention discloses a method for machining an MEMS resonant structure. The method includes: providing silicon wafer as substrate silicon, and growing a first mask layer on the surface of the substrate silicon; machining open patterns on the first mask layer; removing parts of the first mask layer and the substrate silicon which are corresponding to the open patterns by dry etching, and forming groove structures on the substrate silicon; growing second mask layers, forming the second mask layers on groove side walls of the groove structures and the groove bottoms, and forming a composite mask layer on the surface of the substrate silicon; removing the second mask layers by dry etching, and completely removing the second mask layers of the groove bottoms; etching the substrate silicon again by dry etching, enabling the groove structures to be deepened, and enabling newly etched groove side walls not to be covered by mask layers; by wet etching, enabling the inside of the substrate silicon to be communicated with the open pattern to form a cavity; depositing lower electrodes, piezoelectric function materials and upper electrodes; and patterning and releasing the resonant structure by dry etching.