The Niukutou deposit, situated within the Qimantagh ore-concentrated area of the East Kunlun Orogenic Belt (EKOB), represents a typical skarn-type Pb-Zn-(Fe) deposit that is also associated with cobalt (Co) mineralization. The main ore minerals include galena, sphalerite, magnetite, hematite, Co-bearing arsenopyrite, cobaltite and glaucodot. This study conducted geochronological and chemical composition analyses of multi-generational garnets from the deposit, aiming to elucidate their genetic significance in the mineralization process. Field and mineralogical observations indicate the presence of three generations of garnets: Grt-I, Grt-II, and Grt-III. The earliest garnet generation (Grt-I) formed during the prograde stage, typically in garnet skarns, and is often replaced by epidote. The second generation (Grt-II), which coexists with pyroxene, also formed during the prograde stage, whereas the third generation (Grt-III) is associated with pyrrhotite stockworks, suggesting its formation during the sulfide stage. Using in-situ LA-ICP-MS U-Pb dating, garnets yield ages of approximately 230–234 Ma, which aligns with the age of 231.8 ± 7.5 Ma obtained from hydrothermal titanite in the deposit. These ages, combined with those of the previous studies, indicate major magmatic and metallogenic activity of 220–240 Ma in the Qimantagh area. Each generation of garnets displays oscillatory zoning characterized by alternating andradite and grossular compositions. The variations in Sn and high field-strength element (HFSE) contents across different garnet generations indicate an increasing trend in oxygen fugacity as mineralization progresses. The high Sn contents in the Niukutou garnets provide geochemical clues for the potential of Sn-W mineralization in this deposit, which should pay attention to in future exploration. Additionally, the high As concentrations in the Niukutou garnets suggest an As-rich hydrothermal fluid, which, owing to the stronger affinity of cobalt for sulfarsenides over sulfides, provides a geochemical indicator for the formation of abundant Co-bearing sulfarsenides rather than cobaltiferous sulfides in the deposit.