Glass has excellent advantages of high-frequency electrical properties, mechanical stability and low cost, making it an ideal material for the next generation of high-density packaging substrates. However, there is a significant difference in the coefficients of thermal expansion between glass and copper, considerable thermal stress is prone to occur during temperature changes, especially near key structures such as through glass vias (TGVs), which affects the performance and reliability of the glass substrate. Aiming at the reliability issue of the glass substrate hole-filling structure, the finite element simulation and experimental methods are used to study the introduction of an organic polymer layer at the interface between glass and copper as a stress buffer layer to regulate the internal stress at the interface and improve its reliability. The influence law of the organic polymer thickness on the thermal stress in glass filling structure is analyzed. The simulation results show that inserting a buffer layer with a thickness of 1 μm can reduce the maximum principal stress of the glass substrate by approximately 40%. The experiments further verify that the thermal stress reliability of the glass substrate with a stress buffer layer has been significantly improved.