Rationale Gas chromatography‐mass spectrometry (GC‐MS) is an analytical technique widely used in materials science, biomedicine, and other fields. The target compound in the experiment is identified by searching for its mass spectrum in a large mass spectrum database using some algorithms. This work introduces the use of deep learning ranking for the identification of small molecules using low‐resolution electron ionization MS. Because different spectra are often very similar, the algorithm produces wrong search results, and the search accuracy needs improvement. Due to the library's large amount of data, the algorithm sometimes requires a large amount of calculation and is very time consuming. Methods Given these two problems, this work aims to develop a model for ranking based on mass‐to‐charge ratio (m/z) pre‐retrieval method combined with deep learning to improve search accuracy and reduce the algorithm's computational time. The master spectral library maintained by the National Institute of Standards and Technology is used as the reference library for all the experiments, and the replicate library is used as the query library to evaluate the method's performance. Results Compared with non‐machine learning algorithms, the combination of m/z matching pre‐retrieval and deep learning significantly improves library retrieval accuracy by about 4%. Moreover, compared with the deep learning sorting algorithm that does not use the pre‐retrieval process, it improves the accuracy of spectral library retrieval by about 0.1% and reduces the computational time of the algorithm by more than 2 h. Conclusions This method identifies compounds more efficiently and accurately than non‐machine learning and deep learning algorithms without a pre‐retrieval process.