This study addresses an intermodal routing problem encountered by an intermodal transportation operator fulfilling the food grain transportation order of an agri-food company. To enhance the environmental sustainability of food logistics, carbon tax and trading regulations have been employed to reduce the carbon emissions associated with transportation. Multi-source uncertainties, including the company’s demand for food grains and various parameters related to the intermodal transportation activities, are modeled via trapezoidal fuzzy numbers to optimize the comprehensive reliability of the solution. This work incorporates wastage reduction by lowering the wastage costs and formulating a wastage threshold constraint in intermodal routing. Accordingly, a fuzzy mixed-integer nonlinear programming model for a green and reliable intermodal routing problem for food grain transportation is proposed. To overcome the model’s insolvability and the difficulty in finding the global optimum solution to a nonlinear optimization model, a two-stage solution method is developed, employing chance-constrained programming and linearization technique to reformulate the initial model. A numerical case study is given to verify the feasibility of the proposed methods. Sensitivity analysis reveals the influence of confidence levels and wastage threshold, providing insights for the agri-food company to balance economics, reliability, and wastage reduction in food grain transportation. The numerical case study also analyzes the feasibility of carbon tax and trading regulations in reducing carbon emissions, concluding that carbon tax regulations consistently achieve greater reductions and are universally feasible. In contrast, the feasibility of carbon trading regulations depends on confidence levels and wastage threshold. The findings of this work could provide strong quantitative support for intermodal transportation operators and agri-food companies seeking to implement sustainable food grain transportation.