Weathering features of sandstone heritage can be recognized by using artificial intelligence (AI) based surrogate models, and most models perform classification tasks for types based on precise labels. But there are lack of prior validated knowledge of the weathering or untagged historical data for complex weathering conditions in many cases. To this aim, a unsupervised graph neural network (GNN) based on the statistical features of the acoustic emission (AE) signals is constructed. Firstly, taking unweathered sandstone as a reference, we define 4 weathering levels of sandstone ranging from I to IV based on pore indicators. We selected 11 statistical features that are high correlated with pore of sandstone. Then, this GNN is constructed and trained by 2880 sets of statistical measured AE signals. Compared with AEs, LOF and IF models, GNN achieves the best identification performance among the four evaluation criteria. Each iteration of the GNN network is fitting the feature information of the signals and their neighbors. By data dimensionality reduction techniques, when the GNN stops iterating, it will be easy to distinguish unweathered AE signals from weathered one by comparing the reconstruction error of each signal. Furthermore, when the nearest neighbor’s k gradually increases, the AUC of GNN also gradually increases and then tend to stable when k equals to 50–100. While the hidden layers of the network aggregates less information about the neighborhood features of the signals and cannot distinguish significantly between unweathered and weathered signals when the value of k is small. As the depth of the network deepens, the feature values between signals become more and more similar, their reconstruction errors in the output layer of the network to become more similar, making it difficult to distinguish unweathered AE signals from weathered AE signals via GNN. Meanwhile, GNN adopts more AE features and considers the similarity between each features. This can greatly eliminate various errors caused by wave velocity measurement, greatly improving the robustness of AE detection. Hence, the GNN model presented addresses the limitations of relying solely on P-wave velocity measurements to assess the degree of sandstone weathering at stone cultural heritage.