Recent advances in learning multi-modal representation have witnessed the success in biomedical domains. While established techniques enable handling multi-modal information, the challenges are posed when extended to various clinical modalities and practical modality-missing setting due to the inherent modality gaps. To tackle these, we propose an innovative Modality-prompted Heterogeneous Graph Learning (MERGE), which embeds the numerous disparate clinical modalities into a unified representation, completes the deficient embedding of missing modality and reformulates the cross-modal learning with a graph-based aggregation. Specially, we establish a heterogeneous graph embedding to explicitly capture the diverse semantic properties on both the modality-specific features (nodes) and the cross-modal relations (edges).Then, we design a modality-prompted completion that enables completing the inadequate graph representation of missing modality through a graph prompting mechanism, which generates hallucination graphic topologies to steer the missing embedding towards the intact representation. Through the completed graph, we meticulously develop a knowledge-guided hierarchical cross-modal aggregation consisting of a global meta-path neighbouring to uncover the potential heterogeneous neighbors along the pathways driven by domain knowledge, and a local multi-relation aggregation module for the comprehensive cross-modal interaction across various heterogeneous relations. We assess the efficacy of our methodology on rigorous benchmarked experiments against prior state-of-the-arts. In a nutshell, MERGE represents an initial foray into the intriguing realm of embedding, relating and perceiving the heterogeneous patterns from the various disparate clinical modalities holistically via the graph theory