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The 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. Plain Language Summary: Understanding how earthquakes occur and generate hazards in complex fault systems is challenging. The Kongur Shan Extensional System (KSES) in the northeastern Pamir, with complex fault geometry and variable surface loads around it, is an ideal place to study this problem. Here, we explore three sites in the northern KSES to study past earthquakes: deformed lake sediments in the Muji Basin, the northern Kongur Shan Fault (KSF), and the eastern Muji Fault. The deformed lake sediments show evidence of two large earthquakes around 700 and 1,000 years ago, 230–330 years apart. The other sites also had large earthquakes but with much longer gaps between them. The northern KSF had four earthquakes in the last ∼4,800 years, averaging 1,000–1,870 years apart. The eastern Muji Fault had two earthquakes in the last ∼2,700 years, averaging 1,200–3,000 years apart. The eastern Muji Fault's long gaps between earthquakes suggest they happen irregularly, which might be because the fault is immature and interacts with other faults, plus changes in the weight of the water and glaciers around the fault. Key Points: Three field sites in the northern Kongur Shan Extensional System (KSES) reveal earthquake intervals of 230–330, 1,000–1,870, and 1,200–3,000 years, respectivelyThe eastern Muji Fault in the KSES appears to have "clustered" earthquake recurrenceThe irregular recurrence behavior may be influenced by fault maturity, interaction, and changes in paleolake and/or glacier loads [ABSTRACT FROM AUTHOR]