In proteomics, de novo sequencing is one of the most important methods for peptide sequencing by tandem mass spectrometry. It has the advantage of being independent on any protein databases and plays a key role in the determination of protein sequences of unknown species, monoclonal antibodies sequencing and other fields. However, due to its complexity, the accuracy of de novo sequencing is much lower than that of the database search methods, therefore the wide application of de novo sequencing is limited. Focused on the issue of low accuracy of de novo sequencing, denovo-GCN, a de novo sequencing method based on Graph Convolutional neural Network (GCN) was proposed. In this method, the relationships between peaks in mass spectrometry were expressed by using graph structure, and the peak features were extracted from each corresponding peptide cleavage site. Then the amino acid type at the current cleavage site was predicted by GCN, and finally a complete sequence was formed step by step. Three significant parameters affecting the model were experimentally determined, including the GCN model layer number, the combination of ion types and the number of spectral peaks used for sequencing, and datasets of a wide variety of species were used for experimental comparison. Experimental results show that, the peptide-level recall of denovo-GCN is 4.0 percentage points to 21.1 percentage points higher than those of the graph theory-based methods Novor and pNovo, and is 2.1 percentage points to 10.7 percentage points higher than that of DeepNovo, which adopts Convolutional Neural Network (CNN) and Long Short-Term Memory (LSTM) network.