Structures being used in space environment, should be designed to have minimum CTE(coefficient of thermal expansion) for the dimensional stability. Accurate CTE data of the materials are required to design the space structures consisting of various materials. There are uncertainties in the characteristics of materials even though the same manufacturing processes are applied. Therefore, it is needed to measure the thermal deformation of not only the material specimen but also substructures in simulated space environment, such as high vacuum condition. In this research, therefore, precise CTE measurement system using displacement measuring interferometer and vacuum chamber has been designed with uncertainty analysis of the measurements. This system can be used to measure the CTE of the specimen or thermal expansion of the substructure with varying size up to 50cm in length. To measure the low CTE material, overall uncertainty of this system is expected under 0.01ppm/K.