The >500-km-long Central Qiangtang metamorphic belt (CQMB), northern Tibet, offers valuable materials for studying the tectonic evolution and paleobiogeography of the Qiangtang Block. In this study, two conodont faunas (the Mesogondolella and Clarkina–Hindeodus–Isarcicella faunas) are reported for the first time, from the Jiaomuri area of the CQMB. The Mesogondolella fauna, including M. siciliensis, M. qiangtangensis, and?M. sp., is from the exotic limestone blocks at the Jiaomuchaka 2 and Jiangaizangbu sections, indicating a late Kungurian age (Cisuralian, Early Permian). A total of 20 conodont species from five genera are identified and two conodont biozones are established in the Clarkina–Hindeodus–Isarcicella fauna at the Jiaomuchaka 1 section. In addition, the Borinella nepalensis horizon is also recognized at the present section. Based on the conodont succession, the Permian–Triassic boundary (PTB) is temporarily placed between the Clarkina yini and Isarcicella staeschei zones. The late Kungurian Mesogondolella fauna belongs to a transitional zone between the warm- and cool-water conodont provinces and is slightly different from faunas in the southwestern part of the South Qiangtang Block (SQB). A potential explanation for this phenomenon is that the SQB may have undergone anticlockwise rotation during northward-drifting, and warm-water currents along the northern peri-Gondwanan margin may have played a crucial role in conodont distribution. The absence of coeval cool-water Vjalovognathus and M. idahoensis in the CQMB and the southern part of the SQB suggests a weak paleobiogeographical affinity with the Lhasa Block, eastern Myanmar, and Western Australia. In the Clarkina–Hindeodus–Isarcicella fauna of the PTB interval, the co-existence of the endemic species C. sosioensis and warm-water Iranognathus may indicate that the SQB drifted to equatorial regions and had a close relationship with Iran. In addition, the existence of Borinella confirms that the genus preferred relatively cool-water habitats in the Induan–Olenekian boundary (IOB) interval.