In this study, it is aimed to establish a novel method based on a deep‐learning‐guided surface‐enhanced Raman spectroscopy (SERS) technique to achieve rapid and accurate classification of vaginal cleanliness levels. We proposed a variational autoencoder (VAE) approach to enhance spectral quality, coupled with a deep learning algorithm long short‐term memory (LSTM) neural network to analyze SERS spectra produced by vaginal secretions. The performance of various machine learning (ML) algorithms is assessed using multiple evaluation metrics. Finally, the reliability of the optimal model is tested using blind test data (N = 10/group for each cleanliness level). The data quality of the SERS fingerprints of four types of vaginal secretions is significantly improved after VAE decoding and reconstruction. The signal‐to‐noise ratio of the generated spectra increased from the original 2.58–11.13. Among all algorithms, the VAE–LSTM algorithm demonstrates the best prediction ability and time efficiency. Additionally, blind test datasets yielded an overall accuracy of 85%. In this study, it is concluded that the deep‐learning‐guided SERS technique holds significant potential in rapidly distinguishing between different levels of vaginal cleanliness through human vaginal secretion samples. This contributes to the efficient diagnosis of vaginal cleanliness levels in clinical settings.