The Millennium Eruption (ME) of Changbaishan volcano (Baitoushan, Paektu) at 946 CE (Common Era) is one of the largest explosive eruptions on Earth during Holocene times. We date unpolished zircon crystal faces from diverse ME products collected from the southern side of Changbaishan volcano where the ME pumice and welded and non-welded pyroclastic flow deposits (PFD) are better exposed. All zircons from a pumice sample of the southern caldera rim and the youngest (Group 1) zircons from a welded pumiceous PFD sample yield an isochron crystallization age of 0.7 ± 1.8 ka (2σ). Zircons from the welded pumiceous PFD sample yield additional two age groups at ~10 ka and ~ 100 ka. Zircons from a non-welded charcoal-containing PFD have only one age population at 100 ka. Our work shows that different eruption products from ME have different zircon surface age distributions and may tap different levels of a zoned felsic magma chamber. In addition, the results indicate that ion microprobe U-Th dating of zircon crystal surfaces from ME pumices can effectively date the Millennium eruption age. Previously reported zircon U-series ages for Qixangzhan eruption (12.2 ± 1.1 ka, 2σ) and Yuanchi eruption (7.3 ± 1.8 ka, 2σ) at Changbaishan are also likely to date their respective eruption ages. The occurrence of 100 ka zircons in welded and non-welded PFDs reveals an important magmatic event for the Changbaishan volcano. Zircon and Fe-rich clinopyroxene crystallized at similar temperature at 770–750 °C, indicative of early zircon crystallization in peralkaline magmas. Another important result is the extremely low oxygen fugacity (fO₂ = ΔFMQ-2) of the Changbaishan samples. Minerals in ME magmas were crystallized under some of the most reducing magmatic environments on Earth. Highly reducing conditions of magmas from Changbaishan supports a continental rift setting and argues against significant involvements of subduction-related oxidizing fluids during magma genesis.