The vibration-based method is widely applied to estimate cable tension in cable-supported bridges, but its accuracy can be affected by intricate boundary conditions and errors in flexural stiffness estimation in practical applications. This research group recently introduced a method based on multiple vibration measurements to improve tension estimation accuracy by incorporating the cable’s modal frequencies and corresponding mode shapes. The current study aims to further develop the cable tension estimation methodology for application to linked parallel stay cables. A finite element model is established to precisely capture the vibration characteristics of the out-of-plane and in-plane mode shapes of the linked stay cable system. The corresponding effective vibration lengths are then determined to accurately estimated the tensions of the connected strands. The results from the case with a tension ratio of approximately 1:1 between two strands clearly demonstrate the exceptional stability and remarkable accuracy of the developed method. Whether using out-of-plane or in-plane measurements on either of the two strands, the errors in effective vibration lengths consistently stay within ±0.1%.