China currently operates over ten cross-border railways, with container transportation serving as a critical component of transnational rail freight. Following the operational commencement of the China-Laos Railway, challenges have emerged regarding mismatched container specifications at border crossings and the economically efficient repatriation of empty containers stranded in Laos. This study develops an optimization model to determine empty container repositioning routes for transnational railway operations while satisfying container demand at various stations over a specified period. By constructing a multi-layered intermodal network, we formulate a linear programming model with the optimization objective of minimizing total transportation costs for cross-border railway empty container repositioning operations. The study proposes a transportation problem-solving methodology incorporating nodal flow requirements. A case study of the China-Laos Railway demonstrates that direct rail transportation outperforms the highway (Vientiane-Haiphong) - maritime (Haiphong-Qinzhou) - railway (Qinzhou-Kunming) intermodal alternative in both cost efficiency and transit time. The proposed model effectively addresses low container turnover rates in China-Laos Railway operations while providing decision-makers with macro-level insights into empty container flow patterns across temporal phases. This analytical framework supports strategic freight organization and container management.