Macro-level scientific and technological coordination is essential to improve the efficiency of the S&T resources and to make breakthroughs in strategic S&T fields as soon as possible. Both the United States and Japan have strengthened the top-level design of strategic S&T fields at the central policy-making layer, which have played a role in condensing strategic goals, coordinating the implementation of tasks, and allocating S&T resources. Through the official documents of the U. S. and Japan, the paper first introduces the agencies involved in macro S&T coordination mechanism, and studies in detail the personnel composition and responsibilities of the core institutions. Then case study is conducted on the decision-making and implementation process of the latest national strategic plan, aiming to have an insight into the operation of the inter- departmental mechanism. Finally, the common characteristics of the mechanism of the U. S. and Japan are summarized: in strategic S&T fields which reflect the state will, institutions higher than administrative department coordinate administrative, technical and budgetary affairs; The allocation of funds reflects the unity of administrative power and financial power; The high level S&T consulting organization supports making the top-level S&T decisions; Each procedure strives to integrate the consensus and strength of the administrative departments, various industries, and academia. Their experiences provide useful enlightenment for Chinese practice.