Sustainable urban forests require healthy trees with stable structures to improve provision of ecosystem services including air purification and climate mitigation to urban areas. Trees in compact residential areas are particularly prone to development of defects and unstable tree structures. We assessed in detail tree species, key structural and physiological defects, tree dimensions, growing habitats and planting site conditions of 38,156 trees in 102 sampled public housing estates (PHEs) in Hong Kong. The open spaces in PHEs allowed trees to grow in representative urban habitats. PHE attributes including estate age, number of trees, species richness and tree diversity were assessed. The associations among estates, species, tree structure and defects were investigated using Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA). The species-specific approach enlisted tree community, age, DBH and other biomass-structural traits in the data analysis and interpretation. The results showed diverse planting of 202 species from 56 families, with most species beset by multiple defects. The health and structure of two dominant tree species, Acacia confusa and Ficus microcarpa, were respectively influenced by inadequacies and stresses in planting environments, such as inclined surface of disturbed slopes, small pits and planters with poor soil quality, and soil not shielded by groundcover vegetation. Some tree defects of twigs, branches and trunks were associated with tree dimensions, especially tree height and its unnaturally high ratio to crown width and DBH. The findings verified the importance of a species-specific analysis to optimize urban-tree management and maximize benefits to the society.