As the representative of national research institutions, the importance of national laboratories is increasing under the guidance of the new system in which nationwide effort and resources have concentrated on key national undertakings. The development of national laboratories has gradually accelerated in recent years. After years of development, the laboratory′s mission and the boundaries between existing research institutions have become clear, strategic positioning gradually becomes clearly established, but in the actual operation process, there is still controversy between government guidance and free exploration. The direction of scientific research innovation will seriously affect the future function of the laboratory. 
    The development of foreign national laboratories has been for decades. Discussions surrounding the relationship and balance between the two guiding modes have run through the history of the development of national laboratories, greatly promoted the reform and development of the national laboratory system, and can provide important experience for our country. This article analyzes and compares the development history of the National Laboratories under the US Department of Energy, the Department of Defense, and the Helmholtz Association of Germany.
   Each national laboratory system has established the dominant position of government orientation, and the government strictly controls the strategic development direction of the laboratory, while not directly managing daily activities, leaving some free exploration space. Government guidance as the main body is the basic feature of national laboratories as national research institutions, and it is the guarantee to focus the research force on the mission of the institutions, which is conducive to national laboratories focus on the mission of the country and complete the established tasks, but there are many restrictions on researchers, which will easily lead to the decline of scientific research vitality and insufficient scientific research output. Free exploration provides a relaxed space and environment for talent cultivation and cooperation and exchange among academic peers. It acts as a lubricant, which is conducive to driving the enthusiasm of researchers and promoting the development of interdisciplinary disciplines. Researchers take the initiative to carry out research work according to their own will and in accordance with the needs of social development, but it is easy to lead to scattered and mixed research directions. Government guidance and free exploration are not opposite. The pure government guidance and free exploration are not conducive to the development of national laboratories. The combination of the two mechanisms is the only way for national laboratories to maintain a long-term momentum of vigorous development. In terms of details, how much the free exploration space reserved in each national laboratory is different. This is the result of compromise after decades of discussions and reforms, and is compatible with its strategic positioning. 
    The macro development strategy needs a perfect management system to supervise the implementation, and the fund management system is an important part. Macro development concept runs through the construction process of their entire funding management system, and has been rigorously and accurately determined by various rules and regulations.
    Development strategies and management systems need to keep pace with the times. The world′s major national laboratory system generally has a great change in 5-10 years, the strategic goals and management system of national laboratories are not unchanged, and they should keep pace with the times through mutual learning, continuous development and adjustment, all of which are important ways to maintain the vitality of national laboratories.
    These distinctive guidance and control mechanisms for the directions of scientific research and innovation show that there is more than one road to success. National laboratory in our country should be clear in terms of overall development of service objects and accurate positioning by focusing on research, combining closely with national development strategies, playing the role of "national team", taking government guide as the foundation, and implementing national strategies as the goal. At the same time, they should also complete the missions as laboratories make free explorations, and have the most suitable path for their own development. In practice, budget management system should be established to achieve the overall planning of scientific budgeting, to regulate the use of the system, provide loose and orderly budget adjustment, establish a moderate supervision mechanism, for the purpose of reasonable use of funds, legal compliance, implementing national missions and guaranteeing efficiency.