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The composition and structure of the Yarlung Zangbo Suture Zone (YZSZ) provide important constraints on long‐standing disputes about the evolution of the Neo‐Tethys Ocean and continental collision. The Permian tectonic blocks (mainly composed of limestones and volcanic rocks) are widely distributed in the YZSZ. There are still different understandings about the origin of these blocks and their relationship with the evolution of the Neo‐Tethys Ocean. Here, we report the first reliable palaeomagnetic results of the Permian tectonic blocks in the Gyanyima and Mayum areas, the western segment of the YZSZ. Fossil records and our new zircon U–Pb results provide 254–252 Ma and 249 ± 2 Ma age constraints for the strata in the Gyanyima and Mayum sections, respectively. A total of 109 specimens were subjected to stepwise thermal demagnetizations. Among them, 83 specimens yielded interpretable results. After removing a recent geomagnetic field direction at low to intermediate temperature ranges, characteristic remanent magnetization (ChRM) directions can be isolated from the upper Permian–lower Triassic Gyanyima Formation (Fm). Unblocking temperature spectra of the ChRM indicate magnetite and haematite as the main carriers in the basalt and limestone/andesitic‐basalt samples, respectively. The ChRM passed the fold tests and a reversal test at 95% confidence level, indicating that it is most likely a primary remanence. The tilt‐corrected mean direction for 14 sites is D = 18.0°, I = −14.4°, k = 20.5, and α95 = 9.0°, which corresponds to a palaeolatitude of 7.3°S and a palaeopole at 48.3°N, 233.3°E with A95 = 8.1°. Combining the rock assemblage, palaeomagnetic, palaeontological, and geochronologic data, we conclude that these blocks were most likely seamounts formed in the low‐latitude area of the Neo‐Tethys Ocean. The palaeolatitude and origin of these blocks indicate that the evolution of the Neo‐Tethys Ocean was a complex process interspersed with the development of a series of seamounts and microblocks. [ABSTRACT FROM AUTHOR]