Biomedical entity linking aims to map mentions in biomedical text to standardized concepts or entities in a curated knowledge base (KB) such as Unified Medical Language System (UMLS). The latest research tends to solve this problem in a unified framework solely based on surface form matching between mentions and entities. Specifically, these methods focus on addressing the variety challenge of the heterogeneous naming of biomedical concepts. Yet, the ambiguity challenge that the same word under different contexts may refer to distinct entities is usually ignored. To address this challenge, we propose a two-stage linking algorithm to enhance the entity representations based on prompt learning. The first stage includes a coarser-grained retrieval from a representation space defined by a bi-encoder that independently embeds the mention and entity’s surface forms. Unlike previous one-model-fits-all systems, each candidate is then re-ranked with a finer-grained encoder based on prompt-tuning that utilizes the contextual information. Extensive experiments show that our model achieves promising performance improvements compared with several state-of-the-art techniques on the largest biomedical public dataset MedMentions and the NCBI disease corpus. We also observe by cases that the proposed prompt-tuning strategy is effective in solving both the variety and ambiguity challenges in the linking task.