The Beiya Au-base metal deposit in southwest China is characterised by a huge amount of iron associated with gold mineralization. The formation of the Beiya deposit is generally thought to be related to Tertiary potassic intrusion, as porphyry- and skarn-type mineralization are the two most important types of mineralization in the region. However, the lack of direct evidence to constrain the source of iron and gold as well as other metals makes it difficult to accurately conceptualise the ore genesis model. In this study, we report high-precision (0.03 ‰; 2sd) Fe isotope data on Fe-bearing minerals including magnetite, pyrite and chalcopyrite, and major igneous rocks exposed in the area, including monzogranite porphyry (MGP), mafic microgranular enclave (MME), lamprophyre and basalt. Magnetites have a wide range of δ Fe from 0.15 to 0.64 ‰, reflecting substantial isotopic fractionation at different mineralization stages. MMEs have heaviest Fe isotopic composition (0.35 ‰ to 0.88 ‰) compared to MGPs (0.19 ‰ to 0.48 ‰), lamprophyre (∼0.2 ‰) and basalt (∼0.0 ‰). A negative correlation between δ56Fe and TFe2O3 is found for both MPGs and MMEs, which indicates the leaching of iron by hydrothermal fluids mobilizes light Fe and leaves behind isotopically heavy Fe in the remaining source rock. Fe isotopic compositions of MPG and MME overlap with those of magnetite, both of which are proposed to be the source of Fe in magnetite. The basalt has δ56Fe value of 0 ± 0.03 ‰, similar to those of global basalts, suggesting a negligible contribution to the formation of iron ores. Therefore, we propose that magmas parental to the MGP and MME may be the main source of iron to form the Beiya deposit; post-magmatism hydrothermal activities play a key role in leaching the metals out and transporting them to the mineralization area.