Promoting the downscaling and integration of zonal management and control of various environmental pollution sources is an effective way to systematically deal with the current high-intensity and complex environmental problems. Through single-factor and comprehensive pollutant emission intensity evaluation and cluster analysis, we built a full-coverage and cross-scale environmental spatial management and control system for pollution sources, then proposed environmental zoning patterns and pollution control strategies at three scales in the Yangtze River Delta (YRD), China. At the grid scale, the reclassified 7 types of pollution source spaces can be divided into 5 levels based on pollution emission intensity, and the most urgent environmental control subjects can be determined accordingly. Up to the county scale, combined with emission intensity and regional functions, 305 counties can be divided into 5 control intensity zones, which directly correspond to different environmental control intensity, requirements and policies. Finally, at the city scale, 41 cities can be clustered into 7 pollution control zones, which are classified and named as the three-level form of geographic location, development orientation and pollution source characteristics. Fully using the zoning units at different scales of cities, counties and grids can break the limitation of inherent administrative boundaries and allow environmental integration policies to be implemented across departments and regions, also let differentiated policies be more accurately implemented to different administrative levels and pollution source, and then truly improve the efficiency of environmental management. •Geographical spatial structure affects environmental function benefit.•Downscale control system improves environmental management efficiency.•Controlling pollution source spaces through multi-scale zoning.•Inter-city integration zoning breaks the limitation of administrative powers.•Differentiated zoning within county improves the matching of environmental policies.