The present invention is applicable to the technical field of biological information, and provides a protein function prediction method, device, equipment, and storage medium. The method includes: obtaining a protein sequence to be predicted, dividing the protein sequence, obtaining corresponding amino acid fragments, and training Query the word vectors corresponding to the amino acid fragments in a good dictionary, generate the eigenvalues of the protein sequence based on these word vectors, predict the function of the protein sequence according to the eigenvalues of the protein sequence and the trained machine learning model, and generate and output the eigenvalues of the protein sequence Therefore, by obtaining the eigenvalues of protein sequences with context characteristics and performing machine learning on these eigenvalues, the accuracy and efficiency of protein function prediction are effectively improved, and the effect of protein function prediction is improved.