AbstractLow‐velocity zones (LVZ) in the shallow crust such as basins infilled with unconsolidated sediments could significantly amplify seismic waves and cause intense ground motions. In this study, we estimate the seismic site response in the Binchuan basin across the active Chenghai fault zone in northwest Yunnan Province, Southwest China using data from a large‐aperture (∼8 km) dense linear array of 125 three‐component seismometers deployed in 2018 for ∼1 month. We observe that local earthquakes with larger epicentral distances tend to produce stronger spatial variability in peak ground velocity (PGV) across the array. The PGV values are overall larger in the middle of the array than the two sides, especially in the horizontal directions, which is consistent with both tomographic and traveltime results. Using both nearby and distant earthquakes, we find that horizontal ground motions from 0.2 to 2 Hz at stations inside the LVZ are up to 20 times as large as that outside, and a more localized zone (∼500 m wide) enclosing the fault surface trace is characterized by broader frequency bands and larger factors of amplification. As the distance from the fault increases, amplification factors become smaller while the lower limit of the amplification frequency band gradually increases. Variations in predicted ground motion from one‐dimensional SH‐wave modeling reveal amplification and attenuation effects of the LVZ, suggesting that strong lateral heterogeneity should be considered. Our results demonstrate that based on dense array data, analyzing seismic site response is an alternative method to effectively constrain the shallow subsurface fault structure.