With the change in coal supply and demand, the dynamics of multiple transit nodes and the connection between different transportation modes make the Coal Multimodal Transportation System (CMTS) more complicated in the long-distance transportation of coal. Therefore, it is necessary to analyze the multimodal transportation nodes, build a coal multimodal transportation model, measure the network throughput through simulation experiments, and identify system bottlenecks. The CMTS is a complex nonlinear dynamic system with many participants with complex and uncertain links. Different transportation modes, operation links, and connection processes will affect system performance, and modeling and simulation technology effectively study complex dynamic systems. This paper takes the CMTS as the research object, uses agent-based modeling methods and Witness simulation software to analyze the composition and operation mechanism of CMTS, establishes the multiagent model of CMTS, and validates the model by a Witness simulation experiment of northern coal shipped to south. The simulation results indicate the capacity of the transport route and resource utilization of nodes in CMTS in case of different demand growth rates in the future. Based on the multiagent model and Witness simulation results, this paper provides practical support for constructing and applying the multimodal transport system model library and provides the basis for decision-making for the CMTS plan.