The SYNTAX score is a clinically established tool for assessing anatomical lesion complexity in coronary artery disease and guiding subsequent treatment. However, automated SYNTAX scoring is commonly formulated as a direct regression problem from coronary angiography videos to patient-level scores. In this work, we reformulate SYNTAX scoring as a vessel segment identity-preserving anatomical reasoning problem and propose a hierarchical modeling framework that explicitly aligns learning with the clinical workflow. Our approach maintains vessel segment identity across frames and views, estimates stenosis severity at the segment level, and aggregates evidence hierarchically according to coronary anatomy. Simultaneously, to address the scarcity of domain-specific data, we integrate and complete multiple public coronary angiography datasets, constructing a large-scale resource featuring completed vessel segmentation and derived structural annotations. Experiments demonstrate that vessel segment-level stenosis embedding enhances explanatory power and reduces prediction variability compared to baseline models, with the R^2 score improving by 0.201 and dev STD decreasing by 18.4%. These results highlight the necessity of structure-aligned modeling for reliable and stable automated SYNTAX scoring from multi-view coronary angiography videos. The GitHub link is https://github.com/VersaceSu7/SYNTAX_score_777.

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