Transportation systems are fragile when facing various natural hazards. To analyze the performance of these systems under disruption, this paper provides a holistic multi-phase model to assess the resilience of a transportation system consisting of multiple modes. The hazard scenarios for modeling strikes of typhoons are generated by the Spatially Localized Failure (SLF) model and Monte Carlo simulation. Then based on the simulation of typhoon scenarios, we assess the resilience of both single-mode systems and a complementary system of multiple modes. This method is applied to the high-speed rail network and civil aviation network in China under different typhoon intensity scenarios. Results show the different resilience characteristics of the two networks, and more importantly unveil the complementary effect between the two modes when suffering from damages. The improvement of system resilience due to the complementary effects provides a motivation for promoting cooperation between high-speed rail and civil aviation.