Medical entity disambiguation (MED) plays a crucial role in natural language processing and biomedical domains, which is the task of mapping ambiguous medical mentions to structured candidate medical entities from knowledge bases (KBs). However, existing methods for MED often fail to fully utilize the knowledge within medical KBs and overlook essential interactions between medical mentions and candidate entities, resulting in knowledge- and interaction-inefficient modeling and suboptimal disambiguation performance. To address these limitations, this paper proposes a novel approach, MED with Medical Mention Relation and Fine-grained Entity Knowledge (MMR-FEK). Specifically, MMR-FEK incorporates a mention relation fusion module and an entity knowledge fusion module, followed by an interaction module. The former employs a relation graph convolutional network to fuse mention relation information between medical mentions to enhance mention representations, while the latter leverages an attention mechanism to fuse synonym and type information of candidate entities to enhance entity representations. Afterwards, an interaction module is designed to employ a bidirectional attention mechanism to capture interactions between mentions and entities to generate the matching representation. Extensive experiments on two publicly available real-world datasets demonstrate MMR-FEK’s superiority over state-of-the-art(SOTA) MED baselines across all metrics. Our source code is publicly available.