The advancement of Internet of Things (IoT) technologies leads to a wide penetration and large-scale deployment of IoT systems across an entire city or even country. While IoT systems are capable of providing intelligent services, the large amount of data collected and processed in IoT systems also raises serious security concerns. Many research efforts have been devoted to design intelligent network intrusion detection system (NIDS) to prevent misuse of IoT data across smart applications. However, existing approaches may suffer from the issue of limited and imbalanced attack data when training the detection model, which make the system vulnerable especially for those unknown type attacks. In this study, a novel hierarchical adversarial attack (HAA) generation method is introduced to realize the level-aware black-box adversarial attack strategy, targeting the graph neural network (GNN)-based intrusion detection in IoT systems with a limited budget. By constructing a shadow GNN model, an intelligent mechanism based on a saliency map technique is designed to generate adversarial examples by effectively identifying and modifying the critical feature elements with minimal perturbations. A hierarchical node selection algorithm based on random walk with restart (RWR) is developed to select a set of more vulnerable nodes with high attack priority, considering their structural features, and overall loss changes within the targeted IoT network. The proposed HAA generation method is evaluated using the open-source data set UNSW-SOSR2019 with three baseline methods. Comparison results demonstrate its ability in degrading the classification precision by more than 30% in the two state-of-the-art GNN models, GCN and JK-Net, respectively, for NIDS in IoT environments.