For non-destructive testing (NDT) with X-ray computed tomography (XCT), the complex morphological segmentation of homogeneous defects is impossible for traditional threshold-based segmentation algorithm, due to their same absorbances. A variety of defect segmentation using convolutional neural networks (CNNs) has been suitable for such problems, and its accuracy is determined by image quality and comprehensiveness of training set. To achieve a high-performance measurement for quantitative defect evaluation, a modified U-Net-based segmentation model of XCT was proposed suitable for defects with various image quality resulting from different experimental efficiency. The dataset consisting of 24 subsets was acquired from the condition-varying measurements of aluminum alloy samples produced by laser 3D metal printing additive manufacturing. The structure and distribution of segmented pore and crack defects were accurately visualized by our model. Compared with traditional and main CNNs-based segmentation methods, our model exhibited a better recognition accuracy for pores and cracks, the Mean Intersection over Union and Pixel accuracy metrics reaching to 84.83 % and 98.87 % respectively. Practically, the option of efficiency or accuracy priority was quantitatively determined to carry out such a high-performance defect-related NDT. The proposed XCT-based segmentation mode has a great potential in fields of engineering, material science, biomedicine.