Returning extraterrestrial samples to Earth has become essential for future deep space exploration. Achieving a comprehensive evaluation of the physical and chemical properties of samples with minimal damage is key to analyzing extraterrestrial samples in the future, as well as to the future sampling and returning of heterogeneous solid samples. This article aims to reconstruct the three-dimensional internal structure of high-contrast objects, select sections of interest through internal structure and detail features, and then analyze the physical and chemical properties of the samples based on laser spectroscopy technology. This paper proposes a strategy based on Raman mapping and X-ray phase-contrast imaging technology to reconstruct the three-dimensional internal structure of a heterogeneous solid sample and detect the substance composition of the region of interest. This study takes meteorite samples as an example and uses X-ray phase-contrast imaging technology to distinguish and reconstruct the spatial distribution of different components in the meteorite, providing a three-dimensional visualization reference with a high spatial resolution for the spatial positioning of the region of interest. Raman spectroscopy, in combination with LIBS, was used to further identify the meteorite as pallasite and to achieve the spectral image fusion of high spatial and high spectral resolutions. The experimental results show that the unknown meteorite’s three-dimensional structure and its components’ spatial distribution can be evaluated based on Raman mapping combined with X-ray phase-contrast imaging technology. This article provides a highly valuable analytical strategy by which to analyze samples returned from deep space exploration.