When a large number of containers arrive at a node during coal intermodal transportation, it can lead to problems such as container congestion and transfer delays during the transshipment process. Based on this, the criteria importance through intercrieria correlation (CRITIC) objective weighting method was adopted to quantify the risk of transfer delay in coal rail-road intermodal transportation, and then the risk was incorporated into the path optimization factors. Meanwhile, the improved activity-share-intensity-factor (ASIF) equation was introduced to measure the carbon emissions of transportation and transshipment node exchange processes. A carbon emission and transfer delay risk model for the entire freight transportation time was established. Based on the above model, a coal rail-road intermodal transportation path optimization model was proposed, with the objectives of minimizing carbon emissions, transportation costs, transportation time, and transfer delay risk. Through a case study, MATLAB programming was introduced, and the non-dominated sorting genetic algorithm Ⅱ (NSGA-Ⅱ) algorithm was designed to solve the example. The optimization results under different transportation decision conditions were simulated, respectively. By comparing the single-objective optimization results of minimum carbon emissions, minimum transportation costs, shortest transportation time, and minimum transfer delay risk with the multi-objective optimization results that comprehensively consider the above objectives, the advantages of multi-objective optimization in handling low-carbon path optimization for coal rail-road intermodal transportation were explored. The research results show that compared with single-objective optimization, the multi-objective optimization scheme can effectively reduce transportation costs, shorten transportation time, reduce comprehensive energy consumption, and lower the risk of transfer delay, achieving a comprehensive optimal combination of economy and safety in coal rail-road intermodal transportation. At the same time, it also provides a certain reference for the path optimization of rail-road intermodal transportation under different transportation demands and scenarios.