The main dilemmas of the construction of state key laboratories include: 1) the cooperation between competent departments is not close enough; 2) the financial investment is relatively insufficient, and the source of funds is relatively single; 3) the overall scale of laboratories is small, and the research direction and characteristics need to be further defined; 4) the operation mode has not formed a linkage system, and there is a lack of interaction and vitality between laboratories; 5) the advantages of the layout are not effectively highlighted, and the academic growth point of the laboratory is rather vague; 6) the evaluation system needs to be adjusted and the evaluation indexes need to reflect the national mission. Therefore, the reorganization of state key laboratories should adhere to the principles of systematic thinking, integrated planning, synergistic development and integration of advantages, and should specifically: 1) strengthen the planning and coordination of state key laboratories and enhance the coordination and cooperation among competent departments; 2) vigorously increase the financial investment in laboratories and adjust the funding mechanism and mode; 3) identify the development orientation and characteristics of laboratories, adjust the organization form and strengthen international cooperation; 4) strengthen the construction of national laboratory offices and strictly implement the responsibility system of laboratory directors; 5) build top and global research facilities by relying on large-scale projects; 6) the Ministry of Science and Technology should lead the assessment process and the design of the assessment system should reflect the national mission.