Surface ocean primary productivity and biological pump process are key links of global ocean carbon cycle. As one of the major marginal seas in the northwest Pacific, long-term evolution of late Cenozoic paleo-productivity in the Japan Sea closely linked to regional tectonics, East Asian monsoon/westerly, oceanic currents, global climate and sea-level changes. Thus, Japan Sea is an excellent window into the earth system science. Benefit from a series of International Ocean Drilling Programs (DSDP Exp.31, ODP Exp.127/128 and IODP Exp.346) and other post-expedition research, a lot of remarkable recognition has been obtained on the paleoceanography of the Japan Sea, especially on the reconstruction of paleo-productivity. The commonly used proxies of paleo-productivity in the Japan Sea include trace elements, biomarkers, biogenic components and isotope compositions of sediments, and the species and genus of microfossils. On a geologic time scale, Surface ocean primary productivity of the Japan Sea basically depends on the main nutrients (N, P, and Si) and trace nutrients (Fe, Mn, Co, Zn, Cu, etc.) necessary for plankton. And the nutrients in the Japan Sea are mainly carried by wind dust input, volcanic activity, surface ocean currents and deep currents. Consequently, volcanic activity, East Asian monsoon and westerly, ocean current evolution, global climate and sea level change can directly or indirectly affect the supply of nutrients and then change the level of primary productivity in the Japan Sea. At present, reconstructions of the paleo-productivity of the Japan Sea mainly focus on the late Quaternary, lacking for tectonic scale research of the late Cenozoic. In the glacial-interglacial scale, the surface productivity of the Japan Sea is generally weakened during glacial period while increased during interglacial period, mainly depending on the changes in nutrient supply caused by sea water stratification and ventilation conditions. But in tectonic time scale, the long-term evolution of the paleo-productivity in the Japan Sea and its driving mechanism (such as the contribution of wind dust, volcanic iron fertilization and ocean currents) are still unclear, in which regional tectonic evolution, opening and closing of sea channels, global climate and sea-level changes, volcanic activity and evolution of Asian dust input may be crucial driving factors. Due to the lack of calcareous biological deposits in the Japan Sea, diatom fossils show great potential value in further study. In future research, new systematic proxies such as diatom stable isotopes and diatom species assemblage should be developed to reconstruct the long-term evolution history of late Cenozoic paleo-productivity in the Japan Sea; On the other hand, it is necessary to deeply explore the relationship between surface ocean primary productivity, regional tectonic evolution, and global climate change.