The book "Critique of the Quran" written by Dr. Soha has been published in cyberspace in recent years. The author of the book is unknown, then again it’s unknown whether he is a person or a group, Muslim or non-Muslim. In any case, according to the author or authors, there are certain doubts in the Qur'an. This highlights the need to pay attention to the critique of this book. In the meantime, more than a case-by-case response to doubts, it is necessary to identify and critique the intellectual foundations of the author or authors of this book that form the foundations of doubts. In this research, by the method of qualitative content analysis with a conventional approach, the hidden or invisible themes indicating the intellectual foundations that form doubts are revealed. The research findings show7  categories of using unreliable sources, imposing personal views, proposing blasphemous beliefs, denying the principles of belief, scientism and scientific expansionism, not providing scientific and sound documents and not being familiar with the rules of the Qur'anic sciences and its interpretation are the result of a combination of 14 concepts. These concepts resulted from signs. Then from the connection of signs, concepts and categories, the main themes, ie interpretation by personal opinion, the apostasy of the author, the formal rationality of the modern world and the lack of scientific standards of interpretation are obtained. Many doubts can be answered jointly by referring to the obtained categories and themes.