Through-Glass Via (TGV) vertical interconnect copper pillars exhibit significant application prospects in advanced packaging due to their low transmission loss, excellent electrical performance, and potential for high-density vertical interconnection. However, owing to the electrodeposition process used for copper pillar fabrication, a certain proportion of pores exist within the interior. Under long-term current loading, internal pore defects significantly influence electromigration behavior, thereby threatening the service reliability of the interconnect structure. In this paper, a two-dimensional multi-physics coupled electromigration model is established targeting the characteristic of pore segregation along the centerline in TGV copper pillars. The model comprehensively considers the coupling effects among current, temperature, stress, and vacancy transport, and constructs a representative geometry of centerline-segregated pores based on pore profile data. The results indicate that centerline-segregated pores significantly disrupt the current path, resulting in local current crowding in pore expansion regions and local stress concentration in necking regions adjacent to the pores. Compared with uniform structures, centerline-segregated pores cause vulnerable sites to shift from traditional interfaces or end regions toward the interior of the copper pillar, promoting internal void propagation and conductive pathway degradation. This work reveals the mechanism by which centerline-segregated pores influence electromigration failure in TGV copper pillars, providing a theoretical basis for the reliability design of glass-based low-loss vertical interconnect structures.