Nano-kirigami enables direct and versatile shape transformations from two-dimensional predesigns to three-dimensional (3D) architectures in microscale/nanoscale. Here a new and extensible strategy for cascaded multilayer nano-kirigami is demonstrated in a gold/silicon nitride (Au/SiN) bilayer nanofilm for 3D nanofabrication and visible light manipulation. By employing a focused ion-beam-based Boolean irradiation, rich 3D shape transformation and nested multilayer nanostructures are precisely manufactured, which are well reproduced by developing a modified mechanical model. Based on the multilayer and deformable features of the nano-kirigami structures, potentials in manipulating the phase and intensity of visible light are explored. The developed new nano-kirigami strategies, as well as the novel exotic 3D nanostructures, could be helpful to build a novel platform for 3D nanofabrication and find potential applications in microelectromechanical/nanoelectromechanical systems, holographic display, plasmonics, nanophotonics, biophotonics, etc.