The effective segmentation of 3D data is crucial for a wide range of industrial applications, especially for detecting subtle defects in the field of integrated circuits (IC). Ceramic package substrates (CPS), as an important electronic material, are essential in IC packaging owing to their superior physical and chemical properties. However, the complex structure and minor defects of CPS, along with the absence of a publically available dataset, significantly hinder the development of CPS surface defect detection. In this study, we construct a high-quality point cloud dataset for 3D segmentation of surface defects in CPS, i.e., CPS3D-Seg, which has the best point resolution and precision compared to existing 3D industrial datasets. CPS3D-Seg consists of 1300 point cloud samples under 20 product categories, and each sample provides accurate point-level annotations. Meanwhile, we conduct a comprehensive benchmark based on SOTA point cloud segmentation algorithms to validate the effectiveness of CPS3D-Seg. Additionally, we propose a novel 3D segmentation method based on causal inference (CINet), which quantifies potential confounders in point clouds through Structural Refine (SR) and Quality Assessment (QA) Modules. Extensive experiments demonstrate that CINet significantly outperforms existing algorithms in both mIoU and accuracy.