Why is the environmental quality index high in USA, the second most polluting country?
The website you cited has this explanation:


  Most of our data are based on perceptions (opinions) from visitors of this website. For pollution section, we include some relevant data from World Health Organization and other institutions if we find it helpful.


So basically that index is based on people's perception, and CO2 pollution (which your "1/3 of the world total pollution" is probably based on) is not something that people can see or smell, it's problematic because of indirect effects. 

The USA and Europe have pretty strict regulation to reduce the more perceptible components of vehicle and industry exhausts, like soot, sulfur oxides and nitrogen oxides. Their cities also often have good public transportation and zoning laws that separate industry and residential areas.