In the novel A Wrinkle in Time, the "man with red eyes" is the secondary villain, a "front" for IT. He interacts directly with the children, and absorbs Charles Wallace into IT. At one point, he refers to himself as the "Prime Coordinator".
In the movie, the "man with red eyes", also known as Red, actually is the being known as IT. He is a cybernetic organism, half machine, half alien being.