Small-angle X-ray scattering tomography (SAXS-CT) is a non-destructive structural characterization method for nanostructure analysis of heterogeneous materials and its space distribution. The SAXS-CT system based on micro-focusing Kirkpatrick-Baez (KB) mirrors is developed at Shanghai Synchrotron Radiation Facility (SSRF). Samples of Phyllostachys edulis and injection-molded polylactic acid are chosen for experimental verification. The results show that the spot size of the SAXS-CT system can be focused below 20 μm. For the Phyllostachys edulis sample, the position distribution and scattering difference of vascular bundle and parenchyma cell, and the orientation characteristic of nano-fibers are obtained. For the injection-molded polylactic acid sample, the lamella structure inside the sample exhibits the layered distribution characteristic, and the distribution and long spacing of lamella is acquired. The experimental results confirm the reliability and practicality of the SAXS-CT system.