Abstract The petrogenesis of metaluminous to peralkaline high-silica rhyolites in the Cretaceous Yunshan Caldera of SE China has been investigated by analysis of apatite inclusions in zircons and apatite microphenocrysts in volcanic matrices. Zircon-hosted apatite inclusions from both metaluminous and peralkaline high-silica rhyolites are strongly similar, characterized by oscillatory zoning, high light rare earth elements (LREE2O3 3.96–12.1 wt%), Y2O3 (0.48–2.46 wt%), and variable ɛNd(t) values (−10 to +7). In contrast, apatite microphenocrysts are unzoned, have low and concentrated LREE2O3 (≤2.71 wt%) and Y2O3 (≤0.56 wt%), and display uniform ɛNd(t) values (−4.85 to −2.76 in peralkaline and −1.62 to −1.83 in metaluminous high-silica rhyolites). Integrated whole-rock geochemical, petrographic, and thermal constraints indicate that the apatite inclusions are antecrysts, which formed within an early trachytic to low-silica rhyolitic crystal mush, whereas apatite microphenocrysts are autocrysts, which crystallized from the final erupted magmas. In high-silica rhyolites, the coexistence of these distinct two apatite groups provides direct evidence that the high-silica magmas were extracted from a shallow crustal-mush source. The reduction in isotopic heterogeneity from the apatite inclusions in zircon to the apatite microphenocrysts captures the processes of melt accumulation and homogenization, leading to the formation of eruptible rhyolitic magmas. Closed-system differentiation under H2O-undersaturated, F-rich and low-temperature conditions could be the key to the evolution of the interstitial melt of the crystal mush from metaluminous to peralkaline. Comparison between apatite inclusions and microphenocrysts minimizes the influence of mineral-specific crystallization behavior, enabling a more coherent reconstruction of magmatic system evolution. Apatite inclusions in zircon provide a robust tracer of source-region processes. However, their compositions may decouple from those of the erupted magmas, complicating their interpretation in studies of sediment provenance.