"That book is over your head" means that the content or subject matter of a book is too complex or difficult for a particular person to understand. It implies that the book may be too advanced, challenging, or requires specialized knowledge or expertise that the person lacks. The phrase suggests a level of reading comprehension or grasp of the subject that is higher than the person's present understanding or level of education.
When referring to a book specifically, it means the concepts or ideas presented within the book may be beyond someone's current level of understanding or knowledge, or may require a stronger background in a particular subject or more technical proficiency to fully grasp and appreciate its contents.