How do students pursuing a PhD working in research earn money?

Tom explained this nicely. To add one more point, you won't receive a tuition bill, your advisor will. Doing a PhD is less like school as you've experienced so far, and more like working for a small company run by your advisor. The advisor pays your tuition to the university from his or her grant funding, along with what the university charges as overhead. It's almost as if each research group is a franchise, and the university charges a fee so that researchers can use their brand name.

As others have pointed out, schools will describe their stipends, which are designed to cover your living expenses and do so comfortably but simply. They also provide some sort of health care benefits. Serving as a TA is usually required. And, NIH or NSF fellowships can increase both your stipend and provide funding for your research. These fellowships are competitive, so obtaining one is also good for your C.V.

Most universities will offer Ph.D. students a combination of fellowships and teaching stipends to cover the cost of the Ph.D. program. The fellowships and stipends should cover most, if not all, of the cost of the program. When you are accepted to a Ph.D. program, the acceptance will include an explanation of the financial terms you are being offered and then you can decide if the offer will provide enough for your situation.