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Three-dimensionality (3D), the main feature of urban morphology since rapid urban development, has been a trending topic on urban morphology research. Many 3D morphological indices have been proposed to describe urban morphology in current studies. However, the understanding of those indices is independent and isolated, and the spatial relationship of these indices is rarely considered, which makes it difficult to grasp the overall morphological characteristics and its spatial structure. Based on 3D buildings in the central area of Chengdu City, nine morphological indices are constructed. Then, a spatially constrained multivariate clustering method is applied for the comprehensive regionalization of urban morphology after index correlation inspection. The results show that: (1) four morphological indices from height, density and volume can effectively describe the characteristics of urban morphology in the study area respectively; (2) similar to the landform map, a ten-region map is generated that can clearly and intuitively demonstrate 3D morphological zones of integrated characteristics; and (3) a "two-ring with multi-sector" spatial structure is further abstracted from the regional map. This study contributes to acknowledging the spatial structure of urban morphology from a vertical perspective, and the framework can be reduplicated in other cities, which are meaningful to urban management, planning, and construction. • The spatial relationship of 3D morphological indices is considered. • A synthesized regional map is generated to show different 3D characteristic zones. • A "two-ring with multi-sector"spatial structure is abstracted from the vertical perspective. [ABSTRACT FROM AUTHOR]