This is a striking metaphor, which seems somewhat confusing when we start to break it down. The speaker doesn’t compare eternity to "deserts," but talks about deserts that are made out of eternity. We don’t know what eternity looks like. It’s an abstract idea, like time. Deserts come in many varieties, but, here, the desert is a symbol of emptiness and loneliness. This line also plays on the idea of an hourglass, and "the sands of time."