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A multi-scale physical process management system is presented in this paper, taking the plug-in hybrid electric vehicle system as the physical interface connecting the macro traffic system to the micro energy conversion process, with the ultimate goal of global energy management in the full temporal–spatial domain for autonomous plug-in hybrid electric vehicles. This novel method adopts a macro traffic flow model at a large time scale, in which only the initial conditions and the traffic information of key road sections are required, and a car following model at the micro scale. Furthermore, local replanning of energy management is carried out by adjusting the power threshold and the efficiency weight through the type of reinforcement learning that is closest to human learning, once a short term speed disturbance is induced by unknown disturbances in the macro traffic flow. Due to the nonlinear relationship between speed fluctuation and power fluctuation, it is necessary to map the vehicle speed and acceleration characteristics to the power characteristics, instead of directly utilizing the traffic model characterized by the speed and acceleration characteristics. The results show that novel multi-scale physical management can achieve a smaller deviation from the global optimal solution and enhanced robustness of global energy management. Additionally, close coupling between the dynamic characteristics of vehicle components and speed fluctuation ensures correct tracking of the optimized target value.