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In three-dimensional structures based on Through Silicon Via (TSV), an important design consideration is coupling noise between TSVs in addition to TSV and Active Circuits. Indeed, it is very important to estimate the mathematical form in the design of reliable 3D-structures. This paper proposes a technique to compute the TSV-TSV noise coupling in addition to the TSV-active circuit noise coupling. First both models are presented, then, the used Finite Difference Time Domain (FDTD) method is explained in detail for TSV-TSV noise, TSV-Active circuit noise, and TSV-TSV noise with interconnect line. To validate the proposed mathematical models, Matlab and Pspice simulation tools are used. The results given by the FDTD method and Pspice tool are presented. These results show that the calculation of the FDTD method and Pspice are in a good agreement.