Spectrum matching is the most common method for compound identification in mass spectrometry (MS). However, some challenges limit its efficiency, including the coverage of spectral libraries, the accuracy, and the speed of matching. In this study, a million-scalein-silicoEI-MS library is established. Furthermore, an ultra-fast and accurate spectrum matching (FastEI) method is proposed to substantially improve accuracy using Word2vec spectral embedding and boost the speed using the hierarchical navigable small-world graph (HNSW). It achieves 80.4% recall@10 accuracy (88.3% with 5 Da mass filter) with a speedup of two orders of magnitude compared with the weighted cosine similarity method (WCS). When FastEI is applied to identify the molecules beyond NIST 2017 library, it achieves 50% recall@1 accuracy. FastEI is packaged as a standalone and user-friendly software for common users with limited computational backgrounds. Overall, FastEI combined with a million-scalein-silicolibrary facilitates compound identification as an accurate and ultra-fast tool.