Domain-specific documents cover terminologies and specialized knowledge. This has been the main challenge of domain-specific document retrieval systems. Previous approaches propose domain-adaptation and transfer learning methods to alleviate this problem. However, these approaches still follow the same document representation method in previous approaches; a document is embedded into a sing-le vector. In this study, we propose VKGDR. VKGDR represents a given corpus into a graph of entities and their relations (known as a virtual knowledge graph) and computes the relevance between queries and documents based on the graph representation. We conduct three experiments 1) domain-specific document retrieval, 2) comparison of our virtual knowledge graph construction method with previous approaches, and 3) ablation study on each component of our virtual knowledge graph. From the results, we see that unsupervised VKGDR outperforms baselines in a zero-shot setting and even outperforms fully-supervised bi-encoder. We also verify that our virtual knowledge graph construction method results in better retrieval performance than previous approaches.