The invention relates to the technical field of semiconductors, and discloses a bulk acoustic wave resonator, a manufacturing method thereof and a semiconductor device. The bulk acoustic wave resonator comprises a substrate; and a multi-layer structure which is formed on the substrate, wherein the multi-layer structure sequentially comprises a lower electrode layer, a piezoelectric layer and an upper electrode layer from bottom to top, a cavity is formed between the substrate and the multilayer structure, the lower electrode layer or the upper electrode layer is internally provided with a groove, and the groove is filled with a filling material different from the electrode material of the corresponding electrode layer. According to the resonator, the cavity with the lower half cavity and the upper half cavity is formed, the groove is formed in the lower electrode layer or the upper electrode layer, and the groove is filled with the filling material different from the electrode materialof the corresponding electrode layer, so that a novel bulk acoustic wave resonator structure is formed, and the resonator has relatively good performance.