In the context of increasing support for interdisciplinary education and research, the development of interdisciplinary academic organizations in China's universities will become a breakthrough in the higher education system reform. In fact, China's universities as a whole are currently in the primary transitional stage from the mode of independent discipline to the mode of disciplinary convergence. Some research-oriented and comprehensive universities are changing the mode of their academic organizations from pyramid single discipline to matrix interdiscipline. In the meantime, the longstanding historical maladies in the management system and operation mechanism in those organizations have become structural obstacles for the development of interdisciplinary education and research in China's universities. Therefore, we should design effective transformative strategies for the development of interdisciplinary academic organizations in the universities of our country from the following five perspectives-interdisciplinary strategy, talents training mode, innovation in input mechanism, perfection of the assessment system, and construction of social network.