My sister always keeps her room clean.

Literal

Younger-sister [topic-は] room [object-を] always clean [into-に] keep-in-advance.

きれいにしておく ('keep clean in advance/maintain as clean') combines ~にする ('make into') with ~ておく ('do in advance/keep in a state'). Note the original text has きれいにいておく, which appears to be a typo for きれいにしておく.