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The conglomerate‐sandstone transition (CST) preserved in foreland basins records the stratigraphic equivalent of the gravel to sand transition (GST) which migrates in response to shortening in steady state orogen‐foreland basin systems. Two seismic profiles in the southern Junggar foreland basin provide the first seismic record of migrating CSTs and an opportunity to quantify its migration history in response to the growth of the northern Tian Shan. We identify the horizontal positions of the CSTs based on the distinct seismic signature of conglomerate versus sandstone and estimate their ages according to magnetostratigraphic sections. The linear‐regression analysis reveals that the CSTs migrated northward at 0.4 ± 0.1 mm/yr along 84°E from ∼23 to ∼6 Ma and at 4.0 ± 1.2 mm/yr along 87°E from ∼3.1 to ∼0.7 Ma. The discrepancy relates to variations in crustal shortening along strike of the range. Temporal deviations in the CST positions suggest the second‐order impacts of climatic change. Plain Language Summary: Rivers in foreland basins commonly exhibit a sharp gravel to sand transition of bed sediment (GST), which is preserved in the stratigraphy as the conglomerate‐sandstone transition (CST). Previous studies attribute the migration of the CST in foreland basins to tectonics of the coupled mountain ranges. Migration of the CSTs is considered as a possible archive of long‐term crustal shortening in an orogen‐foreland basin system. In this study, we identify the horizontal position of the CST in the southern Junggar foreland basin north of the Tian Shan based on two seismic profiles. Ages of sedimentary layers imaged by the seismic profiles are estimated according to previous magnetostratigraphic investigations. A linear‐regression analysis between positions and ages of the CSTs indicates the northward migration rates of the CSTs. The rates approximate the long‐term crustal shortening rates in the northern Tian Shan orogen‐foreland basin system. A discrepancy between the migration rates of the CSTs in the eastern and western segments reveals variations in crustal shortening along the range. This work demonstrates that migration of CSTs in a foreland basin setting can act as a proxy of crustal shortening in orogen‐foreland basin systems. Key Points: We provide the first documentation of the migration of the conglomerate‐sandstone transition (CST) preserved in foreland basin successionsThe CST in the southern Junggar foreland basin migrates northward at 0.4 ± 0.1 mm/yr along 84°E and at 4.0 ± 1.2 mm/yr along 87°EDeviations between the measured and predicted CST positions are modulated by climate change [ABSTRACT FROM AUTHOR]