Thermal-mechanical treatment is critical for the synthesis of Cu-Ni-Si alloys with high strength and conductivity. In this work, a high-temperature/short-time pre-aging treatment (600 °C, 10 min) was introduced to the thermomechanical processes of Cu-Ni-Si alloys, and the effects of pre-aging on the microstructure and properties of the alloy were investigated in detail. The results showed that Ni2Si particles precipitated from the matrix during pre-aging, promoting the formation of a nanoscale microstructure after cold rolling (cold rolled by 85% reduction). The pre-precipitated Ni2Si particles that formed during pre-aging consumed part of the dissolved Ni and Si solutes in the copper matrix, resulting in a higher initial conductivity before the final aging process. The grain refinement effect and high deformation-stored energy benefited the subsequent final aging by lowering the aging temperature and improving the alloys’ high performance. This provided a guideline for the design and development of high-strength, high-conductivity copper alloys. The strengthening mechanism and corresponding microstructure evolution are also systematically investigated. The pre-existing Ni2Si particles strongly hinder the mobility of dislocations during cold rolling and retard the recovery of sub-structures at room temperature, leading the grain refinement in the nanoscale.