Today, economic growth and the enhancement of social welfare have led to a significant surge in demand for transportation services. In this context, optimizing logistics costs is a fundamental prerequisite not only for reducing final product prices but also for establishing a competitive advantage and ensuring the sustainability of domestic supply chains. Addressing this challenge requires comprehensive approaches to transportation network optimization. Particularly within the pharmaceutical supply chain, the necessity of achieving timely delivery at minimal cost has rendered the Multi Compartment Vehicle Routing Problem an indispensable strategy. By facilitating the simultaneous transport of diverse products, these vehicles maximize distribution efficiency and enhance customer responsiveness with greater economic viability. This study proposes a novel model for a Multi Compartment Vehicle Routing Problem integrated with multimodal transportation within the supply chain, aimed at minimizing both total network costs and distribution time. The proposed model is solved using the TH multi objective optimization approach via GAMS version 23 software. The computational results demonstrate the efficiency and robustness of the model. Furthermore, to validate its practical applicability, a real-world case study of the pharmaceutical supply chain in Tehran is presented, confirming the model’s effectiveness in optimizing complex distribution networks.