With the continuous increase of signal frequency and device integration density in electronic system, serious coupling noise problem in three-dimensional integration system becomes the bottleneck of system performance. Aiming at the three-dimensional interconnection widely used in integrated technology, which is composed of trough silicone via (TSV) and redistribution layer (RDL), an optimized design scheme for three-dimensional interconnection is proposed based on segmental transmission line (STL). In this scheme, the three-dimensional interconnection is divided into several segments under the STL requirement, and the genetic algorithm (GA) is used to screen the segments transmission characteristics to optimize superposition effect of reflected waves, which can compensate the signal loss in the transmission process. The simulation results show that the scheme proposed in this paper reduce the coupling noise caused by wave reflection, and effectively improve the transmission performance in the three-dimensional interconnect system.