There are several Precambrian microcontinents in the Central Asian Orogenic Belt (CAOB). Across these microcontinents, there are many metasedimentary rocks which were not all deposited in the Precambrian. We report on a field-based petrological and zircon geochronological study of metasedimentary rocks from the Tianshan and Beishan orogens, southern CAOB, in order to reveal the Precambrian affinity and Palaeozoic reworking. Most metasedimentary rocks in the Central Tianshan Block (CTB) and Dunhuang arc accretionary system reveal Palaeozoic records of arc accretion, collision, and postcollisional processes. The zircon age patterns of these metasedimentary rocks in the CTB show strong affinity to the Tarim Craton, whereas those of the Dunhuang arc accretionary system suggest a Mongolian affinity. The CTB constituted an independent microcontinent during the Palaeozoic accretionary process and was transformed into a Japan-type arc until it became amalgamated with the Tarim Block in the late Permian. In contrast, the Dunhuang Block shows a probable Mongolian affinity and was a stable unit during the late Mesoproterozoic to Neoproterozoic until the beginning of CAOB orogenesis.