The Pacific entrance of the Indonesian Throughflow refers to the area composed of the eastern Sulawesi Sea, northern Maluku Sea, and the western Pacific Ocean southeast of Luzon and north of Papua New Guinea. The ocean circulation in this area is very important to global ocean mass and heat balances and to climate changes, but is least observed historically. Based on a review of historical studies in the area and the latest observations during the multiple cruises in the western Pacific Ocean conducted by the Institute of Oceanology of the Chinese Academy of Sciences (IOCAS) since 2010, we give a preliminary description of the multiple-scale characters of the regional ocean circulation, the importance of which on the dynamics study of El Nino and the Southern Oscillation, on the intraseasonal variability, and on the hiatus and expedition study of the global warming are discussed. These western Pacific cruises are supported by the National Science Foundation of China Share Cruise Project, the National Basic Research Program of Global Change Project, and the Strategic Priority Project of the Chinese Academy of Sciences under its first theme Dynamics and climatic effects of the western Pacific main ocean currents and warm pool variability. In the past few years, we have worked with the Research Center for Oceanography of the Indonesian Institute of Sciences (RCO/LIPI) to launch multiple oceanographic surveys in the Indonesian seas and conduct time series measurements in key channels of the Indonesian Throughflow. A mooring array of the largest scale in history has been constructed in the Indonesian seas. Based on the international cooperation, strategic partnership between IOCAS and the RCO/LIPI has been established. The oceanographic data obtained through the international cooperation will provide valuable information to support the study of the variability of the Indonesian Throughflow and its role in climate changes, and to serve the One Belt and One Road national policy.