The Late Ordovician−Early Silurian is a convergence period of multiple events in geological history, including dramatic variations of biology, environment, and geology. Extensive research has demonstrated remarkable fluctuations in ocean chemistry, microbial ecosystems, and biogeochemical elemental cycles experienced. However, the spatial-temporal evaluation of marine primary productivity and its links to organic matter accumulation during this key period remain elusive. Here, we present high-resolution marine primary productivity proxy (organic carbon accumulation rates: OCAR) and geochemical data from the Fengtonggang and Qiliao sections deposited in South China and adopted numerous other coeval sections of geochemical data globally, to improve the understanding of these fundamental scientific questions. The results show that all statistical profiles presented broadly high marine primary productivity before and after the Hirnantian glaciation maximum and low values during the glaciation, and a maximum marine primary productivity typically recorded at the uppermost part of the P.pacificus Zone. The Corg/Ptotal ratios indicate that oceanic anoxia was ubiquitous during the Late Katian to Early Rhuddanian, but strong spatial heterogeneous during the Hirnantian glaciation maximum. The volcanism and nitrogen availability may have played an important role in regulating the variations of marine primary productivity globally. Besides, redox-controlled phosphorus cycling may have also exerted a remarkable influence on marine primary productivity. The high Corg/Ptotal ratios (exceed the Redfield ratio of 106/1) observed in the Wufeng and Longmaxi formations indicate that phosphorus was recycled effectively back to the water column, promoting a positive productivity feedback. By contrast, the low Corg/Ptotal ratios found in the Guanyinqiao Bed reflect phosphorus retention in the sediment, limiting phosphorus recycling back to the water column, consequently restricting the primary production. The enhanced marine primary productivity resulted from nutrient regeneration, ocean anoxia, and high sea level may have led to high organic carbon export and preservation. The consistency between the highest marine primary productivity and the first pulse of mass extinction suggests that eutrophication-induced marine anoxia may have played an essential killing mechanism during the first Late Ordovician mass extinction.