The giant Beiya Au skarn deposit and Machangqing porphyry Cu-Mo-(Au) deposit are located in the middle part of the Jinshajiang–Ailaoshan alkaline porphyry metallogenic belt. The Beiya deposit is the largest Au skarn deposit in China, whilst the Machangqing deposit comprises a well-developed porphyry-skarn-epithermal Cu-Mo-(Au) mineral system. In this paper, we present new allanite U-Th-Pb ages and trace element geochemical data from the two deposits and discuss their respective skarn metallogenesis. Based on the mineral assemblage, texture and Th/U ratio, the allanite from the Beiya and Machangqing deposits are likely hydrothermal rather than magmatic. Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) allanite U-Th-Pb dating has yielded Th-Pb isochron ages of 33.4 ± 4.6 Ma (MSWD = 0.22) (Beiya) and 35.4 ± 9.8 Ma (MSWD = 0.26) (Machangqing), representing the retrograde alteration and magnetite skarn mineralization age of the two deposits. The Beiya and Machangqing alkali porphyry-related mineralization are synchronous and genetically linked to the magmatic hydrothermal activities of the Himalayan orogenic event. Major and trace element compositions reveal that the Beiya allanite has higher Fe3+/(Fe3+ + Fe2+) ratios, U content and Th content than the Machangqing allanite, which indicate a higher oxygen fugacity and F content for the ore-forming fluids at Beiya. Such differences in the ore-forming fluids may have contributed to the different metallogenic scales and metal types in the Beiya and Machangqing deposit.