Three-dimensional (3D) interconnection technology based on glass through vias (TGVs) has been used to integrate passive devices, and optoelectronic devices due to its superior electrical qualities, outstanding mechanical stability, and lower cost. Nevertheless, the performance and reliability of the device will be impacted by the thermal stress brought on by the mismatch of the coefficient of thermal expansion among multi-material structures and the complicated structure of TGV. This paper focuses on thermal stress evolution in different geometric and material parameters and the development of a controlled method for filling polymers in TGV interconnected structures. In addition, a numerical study based on the finite element (FE) model has been conducted to analyze the stress distribution of the different thicknesses of TGV-Cu. Additionally, a TGV interconnected structure model with a polymer buffer layer is given to solve the crack problem appearing at the edge of RDL. Meanwhile, after practical verification, in comparison to the experimental results, the FE model was shown to be highly effective and accurate for predicting the evolution of stress, and several recommendations were made to alleviate stress-related reliability concerns. An improved manufacturing process flow for the TGV interconnected structure was proposed and verified as feasible to address the RDL crack issue based on the aforementioned research. It provides helpful information for the creation of highly reliable TGV connection structures.