Electron ionization-mass spectrometry (EI-MS) hyphenated to gas chromatography (GC) is the workhorse for analyzing volatile compounds in complex samples. The spectral matching method can only identify compounds within the spectral database. In response, we present a deep-learning-based approach (DeepEI) for structure elucidation of an unknown compound with its EI-MS spectrum. DeepEI employs deep neural networks to predict molecular fingerprints from an EI-MS spectrum and searches the molecular structure database with the predicted fingerprints. We evaluated DeepEI with MassBank spectra, and the results indicate DeepEI is an effective identification method. In addition, DeepEI can work cooperatively with database spectral matching and NEIMS (fingerprint to spectrum method) to improve identification accuracy.