Quasi-zero stiffness (QZS) isolators have demonstrated appropriate low-frequency vibration isolation performance without sacrificing the load-bearing capacity. The current ‘combined’ design of QZS isolators, however, suffers from complex mechanisms and cumbersome assembly, requiring the parallel arrangement of both negative-stiffness and positive-stiffness elements. Inspired by the multi-functional integration ability of metastructure, this study explores a lightweight design of three-dimensional (3D) QZS metastructure with ‘monolithic’ beam-like unit cells. The study begins with the optimization design method to reach customizable QZS features in the vibration isolation metastructure for complex working environments. Then, it turns to rapid manufacturing to fabricate the metastructure prototypes, whose static and vibration test results demonstrate good agreements with the analytical and numerical results. In an experiment for the vibration isolation of a typical control moment gyro (CMG) of spacecraft, the QZS metastructure exhibited excellent vibration isolation performance (up to 90% reduction in 100–600 Hz frequency range) with only a 4.5% gain in mass. As such, the proposed 3D QZS metastructure paves a new way to the design of lightweight, compact and broadband vibration isolators.