The co-evolution mechanisms between traffic mobility and disease transmission under resource constraints remain poorly understood. This study proposes a two-layer transportation network model integrating the Susceptible-Infectious-Susceptible (SIS) epidemic framework to address this gap. The model incorporates critical factors such as total medical resources, inter-network infection delays, travel willingness, and network topology. Through simulations, we demonstrate that increasing medical resources significantly reduces infection scale during outbreaks, while prolonging inter-network delays slows transmission rates but extends epidemic persistence. Complex network topologies amplify the impact of travel behavior on disease spread, and multi-factor interventions (e.g., combined resource allocation and delay extension) outperform single-factor controls in suppressing transmission. Furthermore, reducing network connectivity (lower average degree) proves effective in mitigating outbreaks, especially under low travel willingness. These findings highlight the necessity of coordinated policies that leverage resource optimization, travel regulation, and network simplification to manage epidemics. This work provides actionable insights for policymakers to design efficient epidemic control strategies in transportation-dependent societies.