Generating adversarial scenes that potentially fail autonomous driving systems provides an effective way to improve their robustness. Extending purely data-driven generative models, recent specialized models satisfy additional controllable requirements such as embedding a traffic sign in a driving scene by manipulating patterns implicitly at the neuron level. In this paper, we introduce a method to incorporate domain knowledge explicitly in the generation process to achieve Semantically Adversarial Generation (SAG). To be consistent with the composition of driving scenes, we first categorize the knowledge into two types, the property of objects and the relationship among objects. We then propose a tree-structured variational auto-encoder (T-VAE) to learn hierarchical scene representation. By imposing semantic rules on the properties of nodes and edges into the tree structure, explicit knowledge integration enables controllable generation. To demonstrate the advantage of structural representation, we construct a synthetic example to illustrate the controllability and explainability of our method in a succinct setting. We further extend to realistic environments for autonomous vehicles, showing that our method efficiently identifies adversarial driving scenes against different state-of-the-art 3D point cloud segmentation models and satisfies the traffic rules specified as explicit knowledge.