Controversy has long surrounded the reconstruction of the East Asian blocks in the Rodinia supercontinent, which was a coherent large landmass during 900–750 Ma and is now dispersed over all current major continents. The Central Qilian block is a Precambrian microcontinent in the early Paleozoic Qilian orogenic belt, which marks the junction of the North China, South China and Tarim cratons. In this paper, we present a systematic study of the petrology, whole-rock geochemistry, and geochronology of supracrustal rocks from the Maxianshan Group and the Xinglongshan Group in the easternmost part of the block. The metasedimentary rocks from both groups overlie a gneissic granite, which has a zircon U-Pb age of 970 ± 6 Ma with εHf(t) values of −3.5 to + 2.5 and is an I-type granite formed in a back-arc setting. Paragneisses from the Maxianshan Group and micaschists from the lower formation of the Xinglongshan Group have detrital zircon U-Pb ages of 2465–876 Ma that peak at ca. 950 Ma. They show strongly decreasing zircon εHf(t) values of + 0.8 to −11.3 and ages from 1174 Ma to 876 Ma. Their protoliths constituted a sedimentary sequence with a long history of deposition during 1174–911 Ma in a continental arc-related basin. Metabasaltic tuffs from the middle formation of the Xinglongshan Group are tholeiitic with a zircon U-Pb age of 958 ± 9 Ma and indicate a back-arc setting. Metasandstones from the upper formation of the Xinglongshan Group have detrital zircon ages of 2668–732 Ma that peak at 810 Ma and 984 Ma and indicate a passive margin setting. Combining our results with existing data, we propose that the Maxianshan Group and the Xinglongshan Group make up an early Neoproterozoic trench-arc-basin system at a continental margin of Rodinia. Oceanic crust subduction underneath the continent at 1174–896 Ma with formation of a mature continental arc, and continuous subduction from 824 to 735 Ma with opening of the Proto-Tethys Ocean as a back-arc basin are suggested for the formation of the Central Qilian block.