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In three-dimensional integrated circuit (3D-IC) systems that use through-silicon via (TSV) technology, a significant design consideration is the coupling noise to or from a TSV. It is important to estimate the TSV noise transfer function and manage the noise-tolerance budget in the design of a reliable 3D-IC system. In this paper, a TSV noise coupling model is proposed based on a three-dimensional transmission line matrix method (3D-TLM). Using the proposed TSV noise coupling model, the noise transfer functions from TSV to TSV and TSV to the active circuit can be precisely estimated in complicated 3D structures, including TSVs, active circuits, and shielding structures such as guard rings. To validate the proposed model, a test vehicle was fabricated using the Hynix via-last TSV process. The proposed model was successfully verified by frequency- and time-domain measurements. Additionally, a noise isolation technique in 3D-IC using a guard ring structure is proposed. The proposed noise isolation technique was also experimentally demonstrated; it provided -17 dB and -10dB of noise isolation between the TSV and an active circuit at 100 MHz and 1 GHz, respectively.