Urban morphological analytics on buildings is informative for sustainable development. 3D building massing features, such as courtyards and setbacks, reflect spatial organizations and circulations, while influence daylight access, ventilation, and shading. However, existing 3D GIS methods usually overlook such 3D massing features, further obscure morphological analytics and environmental assessment. This article proposes MorphCut, an efficient convex decomposition method that segments 3D shapes into mass-aligned parts. MorphCut leverages key morphological properties—planarity, regularity, and Gestalt laws—after a topological preprocessing step to enable mass-aware decomposition. Experiments on representative samples, ranging from small houses to complex skyscrapers, showed that MorphCut outperformed four baseline methods in (i) balancing convexity and compactness, (ii) aligning decomposed parts with building masses, and (iii) preserving geometric fidelity (average deviation: 0.25 m). An urban-scale validation on datasets from Delft and Hong Kong, comprising over 30,000 buildings across 18.3 km², demonstrated MorphCut’s robustness, scalability, and generalizability. MorphCut successfully decomposed 98% of buildings in low-rise regions (+78% over the second-best method) and 93% in high-rise areas (+2%), completing processing in 13 hours (3 hours faster). These results position MorphCut as a foundational 3D GIS tool for large-scale, mass-aware morphological analysis, with implications for digital twins, sustainable planning, and environmental modeling.