Simulation-based analysis has been used for planning, control, and decision-making support of physical internet enabled logistics networks. However, multiagent modelling and simulation based on micro-level interactions have been rarely developed for the pre-studies of digital transformation of urban rail transit systems. This hinders a wider industrial deployment of agent technology in the physical internet enabled transport infrastructure. To fill in this knowledge gap, this work presents an agent-based simulation that explicitly models the micro-level protocols of mobile recourse units and their interaction with the physical infrastructure in a rail-road intermodal transport network. Parameterisation of the simulation model is changeable to examine the influences of different efficiency factors. This allows understanding of which structural functions and resource configuration would make an impact system-wide. Through a practical application, a multiagent system is developed for modelling and analysis of sustainable logistics with individually operated mobile resource units. An agent-based simulation assessment is performed to quantify the improvement options. The results reveal that the physical internet can prevent trucks from empty driving, which has a positive effect on the sustainable logistics operations. The proposed model can be used to support the deployment and planning of digital transformation that could be implemented in urban rail transit systems serving urban distribution and passenger transport.