The demand for urban ecosystem services increases with the rapid growth of the urban population. The urban forest is a crucial ecosystem services provider in cities. To achieve a better estimation of urban ecosystem services, an understanding of the link between heterogeneity and ecosystem services within cities is needed. Other than street trees and forest remnants, the contribution of dispersed green spaces should also be considered. In this study, a ground-based sample quadrat investigation of trees across a sequence of land types in Kyoto City was applied. The ecosystem services and monetary values of trees were further calculated using a customized i-Tree Eco tool. The ecosystem services calculated include carbon storage and sequestration, air pollutants removal, and runoff reduction. Ecosystem services of different land use classes were compared at both quadrat and single-tree levels. We found no significant difference across land use for all the ecosystem services at the quadrat level. However, ecosystem services were different across land use at the single-tree level. We performed a species-specific analysis and found that the pattern of ecosystem services at the single-tree level across land use varies with both the service tested and species. Our study suggests that the heterogeneity within a city should be considered when estimating urban ecosystem services. The results also provide insight into the urban green space management of Kyoto City.