Steel bridge deck pavements (SBDPs) are susceptible to complex mechanical and service environmental conditions, yet current design methods often struggle to simultaneously capture global bridge system behavior and local pavement responses. To address this issue, this study develops a multi-scale finite element modeling framework that integrates a full-bridge model, a refined girder-segment model, and a detailed pavement submodel. The framework is applied to an extra-long suspension bridge to evaluate the mechanical responses of five typical pavement structural configurations—including double-layer SMA, double-layer Epoxy Asphalt (EA), EA-SMA combinations, and a composite scheme with a thin epoxy resin aggregate overlay. By coupling global deformations from a full-bridge model to the local pavement submodel, the proposed method enables a consistent assessment of both bridge-level effects and pavement-level stress concentrations. The analysis reveals that pavement structures significantly alter the stress and strain distributions within the deck system. The results indicate that while the composite configuration with a thin overlay effectively reduces shear stress at the pavement–deck interface, it results in excessive tensile strain, posing a high risk of fatigue cracking. Conversely, the double-layer EA configuration exhibits the lowest fatigue-related strain, demonstrating superior deformation coordination, while the optimized EA-SMA combination offers a robust balance between fatigue control and interfacial stress distribution. These findings validate the effectiveness of the multi-scale approach for SBDP analysis and highlight that rational structural configuration selection—specifically balancing layer stiffness and thickness—is critical for enhancing the durability and long-term performance of steel bridge deck pavements.