Urban land-use/cover changes and their effects on the eco-environment have long been an active research topic in the urbanization field. However, the characteristics of urban inner spatial heterogeneity and its quantitative relationship with thermal environment are still poorly understood, resulting in ineffective application in urban ecological planning and management. Through the integration of “spatial structure theory” in urban geography and “surface energy balance” in urban climatology, we proposed a new concept of urban surface structure and thermal environment regulation to reveal the mechanism between urban spatial structure and surface thermal environment. We developed the EcoCity model for regulating urban land cover structure and thermal environment, and established the eco-regulation thresholds of urban surface thermal environments. Based on the comprehensive analysis of experimental observation, remotely sensed and meteorological data, we examined the spatial patterns of urban habitation, industrial, infrastructure service, and ecological spaces. We examined the impacts of internal land-cover components (e.g., urban impervious surfaces, greenness, and water) on surface radiation and heat flux. This research indicated that difference of thermal environments among urban functional areas is closely related to the proportions of the land-cover components. The highly dense impervious surface areas in commercial and residential zones significantly increased land surface temperature through increasing sensible heat flux, while greenness and water decrease land surface temperature through increasing latent heat flux. We also found that different functional zones due to various proportions of green spaces have various heat dissipation roles and ecological thresholds. Urban greening projects in highly dense impervious surfaces areas such as commercial, transportation, and residential zones are especially effective in promoting latent heat dissipation efficiency of vegetation, leading to strongly cooling effect of unit vegetation coverage. This research indicates that the EcoCity model provides the fundamentals to understand the coupled mechanism between urban land use structure and surface flux and the analysis of their spatiotemporal characteristics. This model provides a general computational model system for defining urban heat island mitigation, the greening ratio indexes, and their regulating thresholds for different functional zones.