Abstract:Type A Strategic Priority Research Program focuses on the breakthrough of strategic high-tech and major public key scientific and technological issues, and its organization and management is a challenging complex system engineering. This paper takes the program named “Western Pacific Ocean System: Structure, Dynamics and Consequences”(WPOS) as an example, which is the first type A Strategic Priority Research Program launched by the Chinese Academy of Sciences in the marine field, summarizes the characteristics of it’s organization management, expounds the management exploration and practice of establishing scientific organization system, exploring innovative operation mechanism, constructing efficient management mechanism, creating good supporting conditions and realizing resource sharing, and puts forward some reflections and suggestions. The purpose of this paper is to provide useful reference for the implementation of other special program management.