It has been proposed that within the Tarim Basin tectonic activity has been limited since Triassic time. However, on the basis of magnetostratigraphy from the eastern Tarim Basin, which defines the chronology of sedimentation and structural evolution of the basin, we show that the basin interior has been uplifted and partitioned during Quaternary. The magnetostratigraphy was constructed from 2228 samples that yielded acceptable inclination values. Characteristic remnant magnetization (ChRM) with both normal (N1–N11) and reversed (R1–R11) polarity was isolated by thermal demagnetization. The data correlate best with polarity chrons C3r to C1n, which range from 5.39 Ma to recent on the geological time scale 2004 (GTS2004). An abrupt decrease in the sedimentation rate is observed at 1.77 Ma in the Ls1 core. This change does not overlap with known Pleistocene climate-change events. We attribute this sedimentation rate decrease to a structurally controlled local decrease in accommodation space where basin basement uplifts occur. This period of sedimentary environmental change reveals that structural partitioning in the basement of the Tarim Basin occurred since ~ 1.77 Ma, and we speculate that tilting of the Southeast Uplift (a sub-basin unit) within the Tarim Basin began in early Pleistocene time.