The ‘agricultural consequences and cost-benefit analysis’ folder includes a spreadsheet model which provides grain crop yield, N application levels, reactive nitrogen emissions, greenhouse gas emissions, nitrogen use efficiency, etc by grain crop regions under baseline conditions and in five N management scenarios. It also includes the cost-benefit analysis. The ‘plot script’ folder includes all the NCAR NCL scripts that are used to plot main figures in the manuscript. The ‘PM2.5 health analysis’ folder includes the R and NCL code and data for China needed to conduct pm2.5 health analysis. Detailed steps are provided in the read.me file therein.