Software refactoring is an important process in software development. During software refactoring, code smell is a popular research topic that refers to design or implementation flaws in the software. Large class is one of the most concerning code smells in software refactoring. Detecting and refactoring such problem has a profound impact on software quality. In past years, software metrics and clustering techniques have commonly been used for the large class detection. However, deep-learning-based approaches have also received considerable attention in recent studies. In this study, we apply graph neural networks (GNNs), an important division of deep learning, to address the problem of large class detection. First, to support the extensive data requirements of the deep learning task, we apply a semiautomatic approach to generate a substantial number of data samples. Next, we design a new type of directed heterogeneous graph (DHG) as an input graph using the methods similarity matrix and software metrics. We construct an input graph for each class sample and make the graph classification with GNNs to identify the smelly classes. In our experiments, we apply three typical GNN model architectures for large class detection and compare the results with those of previous studies. The results show that the proposed approach can achieve more accurate and stable detection performance.