This paper discussed the differences between five phases theory in Han medicine and seven phases theory in Hui medicine. Seven phases theory in Hui medicine is innovated and developed based on five phases theory in Han medicine. Although the two theories show something in common,there are great differences on concept connotation,zang-fu viscera attachment,four seasons,orientation induction between them. This paper analyzed and compared the differences between the two,in order to deepen the understanding of the two medical theories, learn from each other and make the theoretical system more perfect.