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The difference in the polymer processing conditions can lead to a significant difference in the polymer performance. Structural characterization plays an important role, but it is challenging to determine the relationship between polymer processing and performance. An unprecedented new method in development, small-angle X-ray scattering microtomography (SAXS-CT) shows powerful prospects for revealing the polymer microstructures. This study has been used to analyze the gradient nanostructures of poly(butylene adipate-co-terephthalate) (PBAT) produced by an oscillation shear injection molding (OSIM) with various parameters. The significant benefit of using this approach is that a sample of several millimeters can be virtually divided into thousands of voxels while the nanostructure information in each voxel is extracted nondestructively. For each sample produced by specific OSIM processing, nearly 10,000 two-dimensional scattering patterns are reconstructed, and the detailed three-dimensional distribution of structural parameters, including the long period, lamella thickness, amorphous layer thickness, crystallinity, and orientation are drawn one by one according to the tremendous scattering data. Interestingly, the distribution of these parameters shows a very clear ring band in the cross-section of the sample, and the size of this band varies with the preparation conditions of the samples. Such a phenomenon has never been observed in previous studies using other characterization methods. The results reveal that a high shear time is beneficial for the formation of lamellae in the OSIM-made samples. It also suggests that compared to conventional injection molding (CIM), OSIM processing can generally enhance Young’s modulus of PBAT, and low temperature and high shear duration will greatly boost its tensile strength. The accurate and detailed nanostructure obtained by SAXS-CT paves a new way to establish the relationship between the process technology and the structure of the injection-molded polymer.