Comprehensive signal integrity simulation was introduced in the design of PCI-E3.0 and SAS3.0 channels of high density storage server, which are characterized by complicated structures, high signal speed and long and dense traces. The optimized cost-effective design was obtained by simulating the key items of high-speed PCB design such as topology, material and high-speed via structure. The system performances were then evaluated by full channel active simulation to ensure the stability of the system and reduce the manufacture risks. The signal quality of storage server system totally meets the requirement of PCI-E3.0 and SAS3.0 specifications, verifying the effectiveness and reliability of signal integrity simulation.