This study addresses the environmental pollution caused by structural vibrations and secondary structural noise due to subway operation, as well as the need to ensure the normal operation of newly constructed buildings in earthquake-prone areas under seismic load conditions. Based on a real-world project, the challenges and key issues of vibration isolation, seismic isolation, and vibration control for subway systems are analyzed, and a comparison of potential solutions is conducted. The three-dimensional seismic isolation (vibration isolation) technology is employed to simultaneously simulate the effects of both subway operational excitation and seismic forces on the buildings. Computational analysis and experimental verification indicate that the use of three-dimensional seismic isolation (vibration isolation) bearings can significantly reduce vibration and noise issues caused by subway movements, with a marked decrease in the vibration of teaching buildings and secondary structural noise exceeding allowable limits. Under a rare three-direction seismic event, the application of three-dimensional seismic isolation bearings reduces the peak horizontal acceleration of the upper structure by approximately 60%, demonstrating good horizontal isolation performance. The use of three-dimensional seismic isolation bearings to address the dual control of vibration and seismic effects can substantially save on costs and construction time.