Layer-selective manipulation of magnetization direction in a multilayer magnetic structure offers a way to develop a large-capacity magnetic recording device with multiple recording layers. Here, we use a double-layer perpendicular magnetic nanodot consisting of two layers with low and high perpendicular magnetic anisotropy (PMA) and show that layer-selective magnetization switching can be accomplished by utilizing a microwave-assisted magnetization switching technique. Since the low-and high-PMA magnetic layers have different ferromagnetic resonance (FMR) frequencies, their magnetization excitation that reduces the switching field can be individually induced by adjusting the frequency of the applied microwave field (rf), and this principle allows rf to select the layer to be switched. In addition, by measuring thermally excited FMR signals from the nanodot, we find that the magnetization dynamics of the two PMA layers couple through interactions, and we identify the excitation modes responsible for the layer-selective magnetization switching.