PurposeThe research on structure function recognition mainly concentrates on identifying a specific part of academic literature and its applicability in the multidiscipline perspective. A specific part of academic literature, such as sentences, paragraphs and chapter contents are also called a level of academic literature in this paper. There are a few comparative research works on the relationship between models, disciplines and levels in the process of structure function recognition. In view of this, comparative research on structure function recognition based on deep learning has been conducted in this paper.Design/methodology/approachAn experimental corpus, including the academic literature of traditional Chinese medicine, library and information science, computer science, environmental science and phytology, was constructed. Meanwhile, deep learning models such as convolutional neural networks (CNN), long and short-term memory (LSTM) and bidirectional encoder representation from transformers (BERT) were used. The comparative experiments of structure function recognition were conducted with the help of the deep learning models from the multilevel perspective.FindingsThe experimental results showed that (1) the BERT model performed best, with F1 values of 78.02, 89.41 and 94.88%, respectively at the level of sentence, paragraph and chapter content. (2) The deep learning models performed better on the academic literature of traditional Chinese medicine than on other disciplines in most cases, e.g. F1 values of CNN, LSTM and BERT, respectively arrived at 71.14, 69.96 and 78.02% at the level of sentence. (3) The deep learning models performed better at the level of chapter content than other levels, the maximum F1 values of CNN, LSTM and BERT at 91.92, 74.90 and 94.88%, respectively. Furthermore, the confusion matrix of recognition results on the academic literature was introduced to find out the reason for misrecognition.Originality/valueThis paper may inspire other research on structure function recognition, and provide a valuable reference for the analysis of influencing factors.