The De’erni large-scale Cu-Co-Zn deposit is located within the Animaqing ophiolitic mélange belt on the southeastern margin of the East Kunlun orogenic belt. It represents a relatively uncommon type of ultramafic-hosted massive sulfide deposit (UM-VMS). The mineralization is dominated by dense massive sulfides, commonly accompanied by carbonate vein-type and stockwork mineralization, characterized by significant enrichment in Cu and Co. In this study, in-situ LA–ICP–MS U–Pb dating was performed on hydrothermal apatite from carbonate–chalcopyrite±cobaltite-siegenite veins that cut through massive pyrite ores. The obtained U–Pb age of 125.28 ± 0.87 Ma (n = 30) indicates that the overprinting hydrothermal mineralization occurred in the Early Cretaceous, likely associated with magmatic activity related to post-collisional intracontinental extension following the closure of the Paleo-Tethys Ocean. Apatite trace element geochemistry reveals a pronounced positive Eu anomaly (Eu/Eu* = 8.94–16.28) and a weak negative Ce anomaly (Ce/Ce* = 0.50–0.63), reflecting a relatively oxidizing fluid environment during this mineralization stage. LA–ICP–MS analysis of pyrite reveals significant differences in metal concentrations among different generations: pyrite formed during the serpentinization stage (Py1) is enriched in Ni, Co, and Cu with high variability; pyrite from the exhalative sedimentary stage (Py2) shows significantly decreased Ni contents but marked enrichment in Co and Cu; whereas pyrite formed during the hydrothermal superposition stage (Py3) is depleted in Co, Cu, and Ni. These results further confirm that extensive seafloor serpentinization released ore-forming elements from the ultramafic host rocks. Due to differences in geochemical behavior, Co and Cu preferentially entered circulating seawater and were subsequently enriched and precipitated during hydrothermal exhalative mineralization. Later, under an intracontinental extensional regime in the Early Cretaceous, deep-seated magmatism drove oxidized fluids along major faults, promoting the leaching, mobilization, and re-enrichment of Cu, Co, and Ni. This study enhances our understanding of the ore-forming processes in the De’erni deposit, a unique mineralization type, and provides important insights into the mechanisms of extreme cobalt enrichment in hydrothermal systems.