The large meander (LM) of the Kuroshio western boundary current is well known to influence the local climate, fisheries, and aquaculture by greatly modulating regional heat transport, but its impact on biogeochemical processes remains unclear. Using a high‐resolution numerical ocean model and long‐term observational datasets, we show that the path of the Kuroshio south of Japan determines the extent of the shallow nutricline region, where winter convective mixing replenishes nutrient availability for subsequent blooms of phytoplankton during spring. During the LM phase, this mechanism triggers offshore phytoplankton blooms that can be twice as strong as those during the non‐large meander phase. In contrast, spring blooms are weaker in the nearshore region where the nutricline depth is deeper, which reduces the nutrient supply by winter convective mixing during the LM. The LM also modulates the spatial distributions of primary production, air‐sea carbon flux, and export production. Hence, the Kuroshio path variability has broader implications for marine ecosystems and biogeochemical cycles. The biogeochemical impacts of the Kuroshio LM exert bottom‐up control on regional marine ecosystems that may be disproportionate to its thermal effect, and therefore need to be assessed to understand the LM's overall impacts on fisheries and aquaculture.