Commodification of nature refers to the process of making nature into something that is to be bought and sold.
In this book, Cronon talks about how Chicago became a gateway city. He says that Chicago grew because of "second nature." The railroads and canals that spread from the city linked it to the Louisiana Purchase and even beyond it.
These links allowed Chicago to grow and allowed the Purchase lands to be settled as well. In this process, nature was destroyed and turned into something to be exploited economically.
So Cronon is arguing that Chicago represents this process of people dominating nature. He says that it shows people making nature into something to be bought and sold and he argues that this is something that is dangerous to our entire world.