Individual tree structure mapping in cities is important for urban environmental studies. Despite mapping products for tree canopy cover and biomass are reported at multiple spatial scales using various approaches, spatially explicit mapping of individual trees and their three-dimensional structure is sparse. Here we produced an individual tree dataset including tree locations, height, crown area, crown volume, and biomass over the entire New York City, USA for 6,005,690 trees. Individual trees were detected and mapped from remotely sensed datasets along with their height and crown size information. Tree biomass in 296 field plots was measured and modelled using i-Tree Eco. Wall-to-wall tree biomass was mapped using relationships between field measurements and remotely sensed datasets and downscaled to individual trees. Validation using field-plot measurements indicated that our mapping products overestimated tree number, mean tree height and maximum tree height by 11.1%, 8.6%, and 5.3%, respectively. These overestimations were mainly due to the spatial and temporal mis-match between field measurements and remote sensing observations and uncertainties in tree segmentation algorithms. This dataset enables the evaluation of urban forest ecosystem services including regulating urban heat and promoting urban health, which can provide valuable insights for urban forest management and policy making.