As the northernmost part of the Indo-Eurasian collision belt, the Pamir-Tian Shan convergence zone (PTCZ) is a strategic location for understanding intracontinental deformation. Here we present a magnetostratigraphic investigation of a continuous section from the Baxbulak region, to better constrain regional tectonic history. Rock magnetic analyses indicate that hematite and magnetite are the main carriers of characteristic remanent magnetization. The resulting polarity sequence allows a distinct correlation to the geomagnetic polarity time scale, showing that the section spans the interval of 29.1-20.7 Ma. Rock magnetic results further suggest that paramagnetic and antiferromagnetic minerals dominantly contribute to anisotropy of magnetic susceptibility (AMS) of the sequence. Thus, the AMS would indicate the preferred orientations of the mineral grains that are sensitive to tectonic strain. At around 26 Ma, the grouped principal minimum perpendicular to the bedding diverts to a girdle distribution in a N-S direction, demonstrating the overprint of tectonic fabric to previous weakly deformed sedimentary fabric. This would be interpreted as a marked increase in tectonic strain, consistent with various evidence from the Pamir and the neighboring basin that show the Pamir began to migrate northward. Moreover, the coincident changes in distribution of AMS principal axes, in both direction and magnitude, are comparable to the regional counterclockwise rotations observed from paleomagnetic data, likely related to orogenesis.