Because most of the scientific literature data is unmarked, it makes semantic representation learning based on unsupervised graph become crucial. At the same time, in order to enrich the features of scientific literature, a learning method of semantic representation of scientific literature based on adaptive features and graph neural network is proposed. By introducing the adaptive feature method, the features of scientific literature are considered globally and locally. The graph attention mechanism is used to sum the features of scientific literature with citation relationship, and give each scientific literature different feature weights, so as to better express the correlation between the features of different scientific literature. In addition, an unsupervised graph neural network semantic representation learning method is proposed. By comparing the mutual information between the positive and negative local semantic representation of scientific literature and the global graph semantic representation in the potential space, the graph neural network can capture the local and global information, thus improving the learning ability of the semantic representation of scientific literature. The experimental results show that the proposed learning method of semantic representation of scientific literature based on adaptive feature and graph neural network is competitive on the basis of scientific literature classification, and has achieved good results.