Post-traumatic stress disorder (PTSD) presents with complex and diverse clinical manifestations, making accurate and objective diagnosis challenging when relying solely on clinical assessments. Therefore, there is an urgent need to develop reliable and objective auxiliary diagnostic models to provide effective diagnosis for PTSD patients. Currently, the application of graph neural networks for representing PTSD is limited by the expressiveness of existing models, which does not yield optimal classification results. To address this, we proposed a multi-graph multi-kernel graph convolutional network (MK-GCN) model for classifying PTSD data. First, we constructed functional connectivity matrices at different scales for the same subjects using different atlases, followed by employing the k-nearest neighbors algorithm to build the graphs. Second, we introduced the MK-GCN methodology to enhance the feature extraction capability of brain structures at different scales for the same subjects. Finally, we classified the extracted features from multiple scales and utilized graph class activation mapping to identify the top 10 brain regions contributing to classification. Experimental results on seismic-induced PTSD data demonstrated that our model achieved an accuracy of 84.75%, a specificity of 84.02%, and an AUC of 85% in the classification task distinguishing between PTSD patients and non-affected subjects. The findings provide robust evidence for the auxiliary diagnosis of PTSD following earthquakes and hold promise for reliably identifying specific brain regions in other PTSD diagnostic contexts, offering valuable references for clinicians.