[Objective] This study aims at developing a new argumentative zoning method based on deep learning language representation model to achieve better performance. [Methods] We adopted a pre-trained deep learning language representation model BERT, and improved model input with sentence position feature to conduct transfer learning on training data from biochemistry journals. The learned sentence representations were then fed into neural network classifier to achieve argumentative zoning classification. [Results] The experiment indicated that for the eleven-class task, the method achieved significant improvement for most classes. The accuracy reached 81.3%, improved by 29.7% compared to the best performance from previous studies. For the seven core classes, the model achieved an accuracy of 85.5%. [Limitations] Due to limitation on experiment environment, our refined model was trained based on pre-trained parameters, which could limit the potential for classification performance. [Conclusions] The proposed method showed significant improvement compared to shallow machine learning schema or original BERT model, and was able to avoid tedious work of feature engineering. The method is independent of language, hence also suitable for research articles in Chinese language.