<p indent="0mm">Along with the development of natural science at current stage, interdisciplinary scientific research is an inevitable trend and destiny in pursuit of innovations in science or technologies. Much more evidence (global positioning system, internet, national security, integrated circuit, and robot technology, etc.) has proven that interdisciplinary cooperation is necessary and significant in solving important and complicated scientific problems. Thus, the United State of America (USA) built the Defense Advanced Research Projects Agency (DARPA) in 1958. European Union (EU) started the interdisciplinary scientific research plan of Horizon 2020 and built the European Institute of Innovation and Technology (EIT) in 2008. As well, the developed countries (Germany, United Kingdom, and Nordic countries) established interdisciplinary scientific research agencies sequentially and promoted a series of interdisciplinary scientific research projects. In China, the concept of interdisciplinary scientific research was put forward by Dr. Xuesen Qian at National Interdisciplinary Conference in 1985. In 1997, the National Natural Science Foundation of China (NSFC) initiated the Major Research Plan, which aims at solving the key fundamental problems in national strategy and exploring the scientific frontier in understanding the natural world with the assistance of interdisciplinary cooperation. Besides, the Ministry of Science and Technology (MOST) of China also started the National Key Research and Development Program (SKRD Program) in 2015 to break through the bottleneck of science and technology. Although the concept of developing interdisciplinary science is widely accepted all over the world, interdisciplinary research is still in the initial stage. Due to the division of different disciplines formatted in past decades, the barrier and prejudices between disciplines are inveteracy, which imposes the impediment on interdisciplinary cooperation. Further, the complexity of interdisciplinary scientific research reduces the willingness of scientists, especially young scientists, to work on interdisciplinary science. Even worse, the funding mechanism that conforms to the characteristics of interdisciplinary scientific research has not been formed and is still under exploration. How identifying the characteristics of interdisciplinary research and guiding/fostering its development with funding methodology are challenging. Established in October 2020, the Department of Interdisciplinary Sciences (DIS) at NSFC has clear mission and responsibility of promoting interdisciplinary scientific research in China. Since its establishment, DIS has experienced a process of pioneering explorations in a series of aspects to create the culture for accelerating interdisciplinary cooperation, such as initiating “top-down” design of projects, summarization of scientific issues, selection of outstanding projects, and training of potential talent, etc. To encourage more scientists to get involved in interdisciplinary scientific research, this article mainly introduces the operation mechanism of DIS including its duty, organizational structure, work culture, project settings, development goals, etc. Moreover, to better elaborate the difference between DIS and other departments in NSFC, the novel attempts in funding project management are also carefully summarized, such as the innovations in the proposed project application, proposal evaluations, and project management in the past two years. At last, this article provides the outlook on developing interdisciplinary scientific research, the difficulties encountered in the operation that are difficult to solve under the existing funding mechanism, and the challenges in promoting the development of interdisciplinary science in future. We hope this article can pave the way for developing interdisciplinary science and encouraging interdisciplinary talents in China.