Metro systems provide an efficient, convenient, and expeditious way to travel around crowded routes. Because these systems are established in cities, residential buildings close to metro viaducts are significantly affected by structure-borne noise (SBN). Although most previous studies developed SBN prediction with a focus on the accuracy and computational efficiency of a specific bridge type, only limited studies on parameters for the SBN on bridges were carried out. Thus, eliminating SBN is still a challenging task for both the design and operation phases of bridge design. Therefore, this study integrates simplified experiments with numerical analyses to evaluate the influential parameters on the structure-borne noise level (SBNL) for two types of bridge girders, that is, the double-box pre-stressed concrete girder and the double-box steel girder. The present study also proposes an optimization method for reducing the SBNL in the bridge design and operation phases and identifies the sources of SBN for these two types of bridges. In this paper, the solutions to mitigating SBN are first reviewed and briefly introduced. Theories associated with SBN are then derived and experimentally verified using a concrete or steel plate with a unit area. A hybrid evaluation method is developed to integrate transient finite-element simulation with experimental results, and the main sources (e.g., plate thickness, train speed, fastener stiffness, and track irregularity) that induce SBN are examined by this hybrid method. Consequently, the approach to resolving the SBN problem can be optimally determined. As demonstrated in the results from the hybrid evaluation method, the track condition dominates the SBNL for both types of bridges, and the relationship between train speed and plate eigenfrequency should be carefully investigated to avoid the effect of plate resonance. The pre-stressed concrete box girder is the recommended bridge type for use in urban areas from the viewpoint of minimizing the SBNL.