The Hexi Corridor is located beyond the northeastern edge of the Tibetan Plateau, and it is bounded by a series of active thrusts along the northern margin of the Qilian Shan and the southern piedmont of the Longshou Shan. Historically, five destructive earthquakes have occurred along the Hexi Corridor, which indicates that this region poses high potential seismic risks. The 1609 Hongyapu earthquake occurred along the Fodongmiao-Hongyazi fault in the northern Qilian Shan, China, and it killed more than 840 people and destroyed a large number of buildings. Presently, there are different opinions as to the distribution and length of the surface rupture of this event along the Fudongmiao–Hongyazi fault. Thus, we searched all of the fault scarps on the Holocene surfaces and suspected surface rupture locations related to the 1609 earthquake based on previous studies and developed detailed remote-sensing interpretations along the fault. An abundance of north-facing scarps on the younger fans and terrace faces, slightly higher than the active modern stream bed, were found along the Fodongmiao-Hongyazi fault in the area ranging from the Hongshuiba River (39.52°N, 98.41°E) in the west to the Shuiguan River (39.07°N, 99.37°E) in the east. Based on our research, we estimate a surface rupture length as ∼98 km based on the distribution of the fault scarps on Late Holocene surfaces and constraints provided by age dating. Most of the surface ruptures are preserved as fault scarps and indicate an average vertical surface offset of ∼1.0 m, a value found consistently in three segments of the fault. The surface rupture features indicate that segments of the fault ruptured together coseismically during the 1609 earthquake, i.e., a multisegment rupture. Using the surface fault traces, length of 98 or 90 km (without the Shuiguan River section), dip of 30° inferred from previous reflection profiles, a rigidity of 3.3 × 1010 N/m2, and dip slip average as 1.9 m converted from our observations of the offsets, we computed the magnitude of this event as ca. Mw 7.2–Mw 7.4.