This paper introduces an innovative approach to silicon and glass via inspection, which combines hybrid field microscopy with photometric stereo. Conventional optical microscopy techniques are generally limited to superficial inspections and struggle to effectively visualize the internal structures of silicon and glass vias. By utilizing various lighting conditions for 3D reconstruction, the proposed method surpasses these limitations. By integrating photometric stereo to the traditional optical microscopy, our proposed method not only enhances the capability to detect internal micro-scale defects but also intuitively provides a detailed visualization of depth and edge, which are typically not visible with conventional optical microscopy inspection. The experimental results demonstrated that the proposed method effectively captures intricate surface details and internal structures. Quantitative comparisons between the reconstructed models and actual measurements present the capability of the proposed method to significantly improve the silicon and glass via inspection process. Notably, 3D reconstructions of TSVs and TGVs showed depth discrepancies of under 5% with only minor variations observed in heat-affected zones. Despite slight discrepancies from surface unevenness, the method provides consistent and quantitative depth information. As a result, the proposed method achieves enhanced cost-effectiveness while maintaining high accuracy, consistency, and repeatability, suggesting substantial advancements in silicon and glass via inspection techniques.