Coronary artery disease (CAD) is one of the leading causes of death worldwide. Accurate extraction of individual arterial branches from invasive coronary angiograms (ICA) is critical for CAD diagnosis and detection of stenosis. Generating semantic segmentation for coronary arteries through deep learning-based models presents challenges due to the morphological similarity among different types of coronary arteries, making it difficult to maintain high accuracy while keeping low computational complexity. To address this challenge, we propose an innovative approach using the hyper association graph-matching neural network with uncertainty quantification (HAGMN-UQ) for coronary artery semantic labeling on ICAs. The graph-matching procedure maps the arterial branches between two individual graphs, so that the unlabeled arterial segments are classified by the labeled segments, and the coronary artery semantic labeling is achieved. Leveraging hypergraphs not only extends representation capabilities beyond pairwise relationships, but also improves the robustness and accuracy of the graph matching by enabling the modeling of higher-order associations. In addition, employing the uncertainty quantification to determine the trustworthiness of graph matching reduces the required number of comparisons, so as to accelerate the inference speed. Consequently, our model achieved an accuracy of 0.9211 for coronary artery semantic labeling with a fast inference speed, leading to an effective and efficient prediction in real-time clinical decision-making scenarios.