The North Pacific gyre (NPG) is the Earth’s largest ecosystem which is important for marine nitrogen fixation and sensitive to Asian dust-regulated surface nutrient stoichiometry. Meanwhile, it is one of the least understood regions in the global ocean during the late Pleistocene, due to the extremely slow sediment accumulation and lack of biological material preservation. Our study applying a novel, in-situ uranium-thorium isotope analytical method on ferromanganese crusts provides the first quantitative reconstructions on glacial-interglacial dust flux and export productivity in the central NPG. These results suggest that dust flux over the NPG responds closely to ice-sheet size effects but not to major global cooling in the early glaciation. In contrast, the paired 230Th-scavenging-based biological productivity tracks gyre sea surface temperature rather than dust flux during the last glacial cycle. We observe no correlation between dust flux and export productivity in the NPG, indicating Fe is not the productivity-limiting nutrient in this region on orbital time scales. Instead, these results imply that changes in gyre mixing and mode water formation might have led to stronger glacial biological carbon sequestration, with potentially increased nitrogen fixation under higher eolian input.