She keeps his room clean.

Literal

She [topic-は] his [genitive-の] room [object-を] clean [into-に] is-doing.

Xを Yにしている ('keep X in state Y') is the ~ている form of Xを Yにする ('make X Y'). The ~ている here reads as a habitual/maintained state — not just a one-time act of cleaning, but a sustained routine of keeping clean. 清潔 ('clean, hygienic') is more clinical than 綺麗 ('pretty, clean') — 清潔 emphasizes hygiene, 綺麗 emphasizes appearance. Both are na-adjectives.