In the development of intelligent transportation infrastructure, the industrial control systems (ICS) are encountering significant security challenges. Traditional protection strategies have revealed numerous limitations. This paper investigates the innovative application of embodied intelligence to enhance the safety and stability of transportation infrastructure ICS. By conducting an in-depth analysis of the architecture and characteristics of these systems, and integrating the theoretical foundations of embodied intelligence, we propose a comprehensive embodied intelligence protection model comprising perception, decision-making, and execution layers. The design principles for each layer are elaborated upon in detail, including sensor selection and data acquisition/processing in the perception layer, intelligent decision-making algorithms and security policy formulation in the decision-making layer, and actuator control and response mechanism implementation in the execution layer. Additionally, specific algorithmic formulations for sensing data processing, decision-making, execution control, and other critical processes are provided, such as data fusion, anomaly detection, execution control, and response strategy algorithms. Various test scenarios were established to validate the model. Experimental results demonstrate that this protection model significantly improves the system’s accuracy in detecting security threats and reduces response time. This study offers novel insights and methodologies for enhancing the protection of transportation infrastructure ICS, contributing both theoretically and practically.