AbstractThe intricate and changing stress conditions within complex fault networks pose challenges in understanding earthquake recurrence and seismic hazards. The Kongur Shan Extensional System (KSES) in the northeastern Pamir, characterized by complex fault geometries and potentially variable surface loads in its surroundings, offers an ideal research area. Here we investigate three paleoseismic sites in the northern KSES, including lacustrine seismites in the Muji Basin, secondary fault scarps of the northern Kongur Shan Fault (KSF), and an exposure of the eastern Muji Fault. The seismites, as a regional record, indicate two Mw 6–7.3 paleoearthquakes occurring 720–680 and 1030–940 cal yr BP, with an interval of 230–330 years. The other two on‐fault sites reveal paleoearthquakes with compatible magnitudes but much longer average time intervals (ATI). Secondary fault scarps of the northern KSF indicate four Mw 6.9–7.2 paleoearthquakes since 4.8 ± 0.8 ka, with an ATI of 1,000–1,870 years. The fault exposure of the eastern Muji Fault indicates two Mw 6.8–7.3 paleoearthquakes since 2.7 ± 0.3 ka, with an ATI of 1,200–3,000 years. Using its previously constrained long‐term slip rate of ∼6.3 mm/yr and a simple Monte Carlo simulation of earthquake cycles, the observed ATI of the eastern Muji Fault suggests a “clustered” earthquake recurrence behavior. Such potential irregular earthquake recurrence is likely due to the low maturity and fault interaction in the northern KSES, and climate‐related changes in surface loads of paleolakes and glaciers.