The Haobugao Zn-Fe-Sn deposit is a typical skarn deposit in the southern Great Xing’an Range of NE China. Despite many advances in understanding its genesis, the detailed ore-forming processes of Zn, Fe and Sn are still unclear. Amphibole, a rock-forming mineral, has been well studied as an indicator of diverse magmatic and metamorphic processes; however, the geochemistry of hydrothermal amphibole has previously received less attention. The Haobugao deposit contains two generations of hydrothermal amphibole (Amp-I and Amp-Ⅱ), which provides a good opportunity to use amphibole geochemistry to trace the mineralization process. Early Amp-I coexists with cassiterite, magnetite and quartz, whereas late Amp-II coexists with quartz and sulfides and can be further divided into two subgroups: Amp-Ⅱa (in skarn) and Amp-Ⅱb (in the country rocks of siltstone). The oxygen isotopic compositions of the fluid (δ18Ofluid 2.9‰) responsible for the Amp-I formation indicate that the amphiboles formed from mixed magmatic fluid with meteoric water. Amp-I is LREE-depleted and HREE-enriched with obvious negative Eu anomalies. Amp-Ⅱ is generally slightly LREE-depleted with negative or positive Eu anomalies and positive Ce anomalies. The incorporation of trace and rare elements is mainly controlled by the fluid composition. Detailed petrological observations and amphibole geochemistry, combined with previous research results, confirm that Sn, Fe, Pb and Zn mineralization occurred during a single mineralization event. From the oxide to the quartz sulfide stage, the ore-forming fluid evolved from high-temperature and oxidized conditions with enrichment of Sn, Li, Be and REEs to low-temperature and reduced or oxidized conditions with enrichment of Cu, Co and Zn. The concentrations of Cu, Co and Zn in different amphiboles vary with the mineral crystallization sequence. This study shows that amphibole geochemistry can be useful for tracing fluid evolution and mineralization processes in hydrothermal systems.