The invention discloses a distance optimizing method of through silicon via (TSV) positions in a three-dimensional (3D) integrated circuit automatic layout. The distance optimizing method has wide application to the field of design and manufacture of 3D integrated circuits. In a layout formed after initial locating of common 3D integrated circuit TSVs, the number of the TSVs is big, and distribution of the TSVs in the layout is dense, therefore a problem that the positions of the TSVs are too close occurs. When the 3D integrated circuit is manufactured and produced, manufacturers can not manufacture the layout where gaps of the TSVs are smaller than gap restrain of manufacture process. The method uses a distance method to optimize the gaps of the TSVs, an optimized layout is obtained so as to enable the gaps of the TSVs to meet process manufacture requirements, and manufacture can be finished. In the optimized TSV layout, distance of the TSVs is appropriate, working speed of the circuit can be increased, and crosstalk is reduced.