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This paper forwards a novel wire length calculation algorithm based on TSV position. Typical 2D wire length calculation method such as half-perimeter model does not take via position into account. But in 3D IC placement, TSV position does affect the real wire length which is ignored in previous works. To get accurate wire length data and help 3D placement researches, this paper forwards the TSV based 3D IC wire length algorithm. Experiments are done on folded placement results of IBM placement benchmark circuits. Results shows that this algorithm can effectively identify the difference wire length of the cross wafer net according to the traditional method and calculate it accurately.