The supercontinent Rodinia existed as a coherent large landmass from 900 to 750 Ma and is now dispersed over all current major continents. Controversy has long surrounded the reconstructions of the East Asian blocks in Rodinia, especially the South China craton and nearby microcontinents. The Central Qilian block is a Precambrian microcontinent in the early Paleozoic Qilian orogenic belt, which is located in the northeastern part of the Qinghai-Xizang (Tibet) Plateau and marks the junction of the North China, South China and Tarim cratons. The formation and tectonic affinity of the Precambrian basement in the Central Qilian block is unclear, which affects our understanding of the assembly of Rodinia. The Huangyuan Group and the Maxianshan Group crop out in the eastern part of the block and represent the lower part of the basement. In this paper, we present a systematic study of the petrology, whole-rock geochemistry, and geochronology of amphibolites and orthogneisses from the Huangyuan and Maxianshan Groups. The protolith of the amphibolites was tholeiitic and calc-alkaline gabbro or gabbroic diorite formed in a continental arc environment, with laser ablation–inductively coupled plasma mass spectrometry (LA-ICPMS) zircon U-Pb ages of 967–957 Ma, a wide range of εHf(t) values of –3.74 to +5.06 and TDM1 model ages peaking at 1470 Ma and 1607 Ma. Minor inherited zircon grains with older ages of 1207–1515 Ma were collected from the amphibolites. The primitive magma was derived from partial melting of a spinel-facies fertile (lherzolite) lithospheric mantle that was modified by fluids and melts from a subducted slab. Fractionation of olivine, Fe-Ti oxides and plagioclase played a dominant role in the magma differentiation for gabbroic rocks in the Huangyuan Group, while fractionation of olivine and clinopyroxene controlled differentiation to form Maxianshan Group gabbros. The protolith of orthogneisses includes weakly peraluminous I-type and A2-type granites with consistent LA-ICPMS zircon U-Pb ages of 963–936 Ma, a wide range of εHf(t) values of –3.86 to +6.15 and TDM2 model age peaks at 2001 Ma and 1772 Ma. A few inherited zircon grains yield ages of 1033–2558 Ma. The peraluminous I-type granites resulted from a low-pressure partial melting process and the peraluminous A-type granites were derived from a charnockite source heated by large-scale magmatic underplating. Fractionation of plagioclase, biotite, and K-feldspar from the magma played the main role during the generation of the granitoids. The intrusion of these granites is related to a back-arc extension. It is inferred that the lower part of Precambrian basement of the Central Qilian block is composed mainly of early Neoproterozoic rock assemblages formed in a trench-arc-basin system during the assembly of the Rodinia supercontinent, with probable existence of late Paleoproterozoic to Mesoproterozoic continental nuclei. Combining our results with existing data, we identify a sequence of initial intra-oceanic subduction (ca. 1121–967 Ma) in front of a continental nucleus, continuous subduction of oceanic crust beneath the continental mass with formation of a mature continental arc and a back-arc basin (ca. 967–896 Ma) and continental rifting (<ca. 882 Ma) during the formation of the Central Qilian block. As a mature continental arc after ca. 967 Ma, the Central Qilian block was located at the margin of Rodinia and faced the Neoproterozoic Mirovoi Ocean. The breakup of the supercontinent left the Central Qilian block as a late Neoproterozoic isolated arc terrane.