The layout of precise microelectronic devices in spacecrafts affects local vibration characteristics of the spacecraft. The local vibration characteristics of the spacecraft affect stability and precision of the microelectronic devices. Thus, layout optimization of the microelectronic devices is performed to decrease the effects of local vibration of the spacecraft. In each optimization iteration process, the microelectronic devices are bonded in a flexible panel that fixed on the spacecraft by several bolts. The structure-preserving method, focusing on the local geometric properties of the system, is employed to investigate local vibration characteristics of the spacecraft in each optimization iteration step. The optimization method and associated results presented in this paper provide guidelines on layout optimization of precise microelectronic devices in spacecrafts.