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Global mitigation of greenhouse gas (GHG) emission targets to regional solution at different scales with structural effects. Because local ecosystem service has different functions to influence regional environment, it is unclear that land use structural effects on lowering emission intensity and mitigating air pollution, and it is debatable that the efficiency of mitigation of GHG emission can be improved by increasing what kind of ecological infrastructure at regional scale. We propose a systematic methodology on identification of trade-offs among structural impacts of land use change on emission intensity at regional scale through both qualitatively and quantitatively statistical analysis to clarify impacts of different land use on the mitigation of emission intensity. In particular to a region with some distinct constraints of natural resources, regional planning has to rely on scientific solutions for bridging the gap of emission mitigation target among multi-levels of administrations and at same time enhancing the optimal allocation of natural resource. In this case study, we qualitatively analyze the principle component among impact factors in a regional socio-economic-ecological system of Zhangye City (where is located at the middle reach of the Heihe River Basin) during 1980s–2010s, and quantitatively analyze the relationship between land use structure and emission intensity with controlling the effects of air contaminations. The analytical results prove that forest land has statistically significant impacts on the mitigation of emission intensity, more importantly, there are no statistical significant evidences showing that cultivated land and wetland have the same functions. It indicates that to identify key issues from those mixed impacts of land use structure at regional scale determines to promote an optimal path of natural resource allocation for reducing the GHG emission and air contaminations. It implies that mitigation of GHG sorely needs to take land use structure changes into consideration of the systematic research for scientifically improving regional planning and sustainable development. [ABSTRACT FROM AUTHOR]