The knee joint is one of the tissues that often appear diseased, and the pathogenesis owing to its structure. Therefore, the micro-structure of the knee joint was studied by synchrotron radiation phasecontrast CT imaging (SRPCI-CT). The contrast and the sharpness of the reconstructed slice were calculated and analysed. From these results, the layer structure of the joint tissue can be seen. The cartilage layer (including the meniscus) is about 1.44 mm, and the epiphyseal layer is about 2.25 mm, which conforms to the actual situation of rat knees. From the 3D images, the structure of the meniscus and the epiphyseal bone can be observed. The epiphyseal bone line is also particularly obvious. Simultaneously, the epiphyseal bone also has a mesh structure, which has the characteristics of both cartilage and tibia. Further research on the tibia can determine that the trabecular bone line is about 130 microns. Finally, the bone volume fraction (BVF) of the joint, the data also reflect the existence of a layer structure, and its scale distribution is consistent with the results of sharpness and contrast analysis. The SRPCI-CT can play an important role in the study micro-structure of joints.