The outbreak of diseases is influenced by various factors such as the total amount of resources and individual contacts. However, the co-evolution mechanism between individual travel behavior and disease transmission under limited resources remains unclear. In view of this, we construct a disease transmission model on a two-layer transportation network, considering the comprehensive effects of the total amount of medical resources, inter-network infection delay, travel willingness, and network topology. The simulation results show that increasing the total amount of resources can effectively reduce the disease scale in the transportation network during outbreaks. Additionally, an increase in inter-network infection delay can effectively slow down the disease transmission rate but prolongs the persistence of the disease in the population, affecting the regulation of infection scale by travel willingness. Meanwhile, the more complex the topology of the transportation network, the greater the impact of travel behavior on disease transmission. More importantly, compared to single-factor control, multi-factor combined control is more effective in inhibiting disease transmission. This paper provides new insights into the co-evolution mechanism of traffic travel behavior and disease transmission, and will offer valuable guidance for governments to control epidemic spread through transportation networks.