Multi-organ diseases present significant challenges due to their simultaneous impact on multiple organ systems, necessitating complex and adaptive treatment strategies. Despite recent advancements in AI-powered healthcare decision support systems, existing solutions are limited to individual organ systems. They often ignore the intricate dependencies between organ system and thereby fails to provide holistic treatment recommendations that are useful in practice. We propose a novel hierarchical multi-agent reinforcement learning (HMARL) framework to address these challenges. This framework uses dedicated agents for each organ system, and model dynamic through explicit inter-agent communication channels, enabling coordinated treatment strategies across organs. Furthermore, we introduce a dual-layer state representation technique to contextualize patient conditions at various hierarchical levels, enhancing the treatment accuracy and relevance. Through extensive qualitative and quantitative evaluations in managing sepsis (a complex multi-organ disease), our approach demonstrates its ability to learn effective treatment policies that significantly improve patient survival rates. This framework marks a substantial advancement in clinical decision support systems, pioneering a comprehensive approach for multi-organ treatment recommendations.