The upper mesopelagic ocean is the primary hotspot for the remineralization of exported organic matter, thereby regulating the biological carbon pump. Despite growing recognition of non-Redfield remineralization and mesopelagic nutrient trapping, the vertical structure and spatiotemporal variability of preferential remineralization remain poorly constrained. Using long-term carbonate system and hydrochemical data from the PN-line transect and a ΔDIC/AOU (dissolved inorganic carbon/apparent oxygen utilization) method, we reconstructed the vertical and temporal patterns of preferential remineralization and mesopelagic element stoichiometry. Preferential remineralization of nitrogen-enriched organic matter drives a minimum DIC/DIN (dissolved inorganic nitrogen) ratio at 300 m. This preferential allocation of DIN to the upper mesopelagic waters elevates the N/P (phosphate) ratio, alleviating nitrogen limitation and enhancing Chl a in the euphotic zone. The continued rise in N/P ratio in the euphotic zone is expected to further enhance Chl a in the future.