Martyr Sayyed Mostafa Khomeini is one of the contemporary philosophers who has grown in transcendent philosophy and has new doctrines in Islamic Philosophy. His only remained book, Commentaries on the Transcendent philosophy, contains his theories. But you can also find his special philosophical theories in his 29 volume books about Fiqh, Assets of Fiqh, and Interpretation. His big philosophical book, Philosophical Rules, has missed so in several times his theories have remained without any reason. The writer has written another paper in 32 innovations in Metaphysics and in this article paid attention on 17 innovations in Theology and compared with past philosophers. The doctrines are about various aspects such as: God and his attributes, worlds of existence, and resurrection. The research helps us in compilation the history of Islamic Philosophy.