As the Chinese lunar exploration project prepares for future exploration activities on the Moon, there is a growing need to develop high-fidelity lunar soil simulants. The morphological analysis of lunar soil and its simulant is important for matching the unique properties of the agglutinates. To date, several techniques, including scanning electron, X-ray, and optical microscopies, have been extensively applied to analyze the three-dimensional (3D) morphology of lunar samples. However, none of these tools can acquire the natural color fine 3D microstructure of the samples, which is necessary to analyze components of the lunar meteorite and soil particles. In this letter, we present a high-resolution, natural color 3D tomographic system for the initial analysis of lunar samples. The superior performance of the system is demonstrated by the fine details and color 3D tomography of a lunar meteorite and lunar soil simulant. This method is expected to provide an essential tool for visually presenting the geological evolution of the Moon.