Three-dimensional (3D) isolation bearings are effective means to reduce the adverse effects of metro vibrations on structures. The current research focuses on the relationship between the vertical stiffness and metro vibration isolation performance of bearings, but neglects the vibration filtering effect resulting from the inherent resonance and material damping effect of them. In this study, a novel 3D isolation bearing was proposed, composed of spring bearings (SBs) and laminated nature rubber bearings (LNR) vertically in series (denoted as 3DSL), and not only its vertical stiffness but also vibration filtering effect on metro-induced vibration isolation performance were fully studied. The design principle and vibration isolation mechanism of the 3DSL were described, followed by the design and test of three specimens. After that, a case study was conducted to investigate the influence of the 3DSL's filtering effect on metro vibration isolation. The results indicated that the 3DSL exhibited high vertical loading capacity and low vertical stiffness. Furthermore, it was found that the vibration amplitude was slightly amplified in the low-frequency range (1–50 Hz), while significantly reduced in the high-frequency range (50–200 Hz) due to the vibration filtering effect of the 3DSL. Altogether, these results demonstrated that the excellent metro vibration isolation performance of the 3DSL was attributed to the low vertical stiffness and vibration filtering effect. It is recommended to consider both the reduction of vertical stiffness and vibration filtering effect of 3D isolation bearings when designing isolation systems for metro vibrations.