Air-rail intermodal transportation (ARIT) plays a crucial role in China’s intermodal transportation system. This study aims to model and optimize issues such as inefficiency and complexity in China’s ARIT freight transportation using Business Process Reengineering and Stochastic Petri Nets theories. The Petri Net (PN) model for incoming freight transport in ARIT is based on actual operations, employing a new method involving Stochastic Petri Nets and isomorphic Markov Chains theory for performance analysis. Performance analysis results help intuitively identify areas needing optimization. Based on optimization principles, elements such as railway container packaging are improved, resulting in an optimized PN model for ARIT. Finally, data analysis shows that the optimized ARIT model reduces total delay by 7.7% compared to the original. This demonstrates that the new method, combining Markov Chain performance analysis and optimization principles, is feasible and effective for ARIT optimization.