This paper reviews the relevant ocean dynamics study of the Indonesian Seas and Indonesian Throughflow in the last 30 years. Centred at the heart of Maritime Contininent, the Indonesian Seas connect the Western Pacific Warm Pool and Indian Ocean Warm Pool, having a direct impact on the large scale atmospheric circulations. The Indonesian Throughflow (ITF), weaving through the mutli-straits and passages in the Indonesian Seas, balances the thermal and saline distribution of the world ocean. In a long time scale, ITF has an influence on the structure of general circulation and climate change. Based on the advance of the in situ observation by international cooperation, the global scientific community has a significant advance in the regional oceanography of the Indonesian Seas and ITF. Those studies include two aspects. In the study of the regional oceanography of the Indonesian Seas, this paper reviews the major advance in ocean circulation, wave dynamics, tide and mixing, ocean vertical stratifications and air-sea interactions. In the study of the ITF, which is the only ocean connection of the global conveyer belt in the tropics, this paper review the advance in the ITF pathway, vertical structure, multiscale variations, water mass origin and their influence, heat and saline transport, ITF relationship with the Pacific circulations and Indian Ocean circulations, and its impact on the large scale ocean-atmosphere interactions, etc. This paper categorizes and discusses the relevant study and proposes prospects.