In this paper, a process scheme for polymer TSV fabrication is proposed to solve the difficulty of polymer liner formation in TSV technology. By using ring trench etching and BCB deposition in a vacuum environment, uniform BCB liner can be successfully fabricated. Electrical measurement by using Kelvin structure is completed to ensure the performance of fabrication. However, a new phenomenon causing tiny resistance changes with the arrangement of TSV is discovered during the measurement of TSV chain. In this research, this effect is discussed in detail by designing different design of experiment (DOE) to pursue good electrical connection and reduce the variance of delay property of each TSV. Based on statistical results, impacts of TSV manufacturing process variance are discussed and the guideline in high density TSV design is found.