In this article, a six-degree-of-freedom (6-DOF) micro-vibration platform (6-MVP) based on the Gough–Stewart configuration is designed to reproduce the 6-DOF micro-vibration that occurs at the installation surfaces of sensitive space-based instruments such as large space optical loads and laser communications equipment. The platform’s dynamic model is simplified because of the small displacement characteristics of micro-vibrations. By considering the multifrequency line spectrum characteristics of micro-vibrations and the parameter uncertainties, an iterative feedback control strategy based on a frequency response model is designed, and the effectiveness of the proposed control strategy is verified by performing integrated simulations. Finally, micro-vibration experiments are performed with a 10 kg load on the platform. The results of these micro-vibration experiments show that after several iterations, the amplitude control errors are less than 3% and the phase control errors are less than 1°. The control strategy presented in this article offers the advantages of a simple algorithm and high precision and it can also be used to control other similar micro-vibration platforms.