She looks like his older sister, but she's actually his mother.

Literal

She [topic-は] his [genitive-の] older-sister [like-のように] looks [but-が], actually mother [explanatory-なのだ].

Two clauses contrast appearance and reality. ~のように見える ('looks like') sets up the deceptive appearance. 実は ('actually, in fact') flags the upcoming truth. The sentence-final ~なのだ (or contracted ~なんだ) is the explanatory copula — adds emphasis and 'here's the explanation.' The clause-final が functions as the soft contrastive 'but' connecting appearance to reality. A textbook example of the 'looks like X, but actually Y' pattern.