In the 2010 Maule, Chile, earthquake (Mw 8.8), many high‐rise buildings in downtown Concepción (CONC) sustained severe damage. The accelerogram observed at CONC had large amplitudes and long periods. The spectra contained strong peaks with periods around 2 s, whereas the spectra from a neighboring site (CCSP) did not exhibit strong peaks. Because CONC and CCSP are located in the Concepción basin and at the edge of the basin, respectively, these observations suggest that the spectral differences are due to site geological effects. To quantitatively evaluate site effects, microtremor array observations were conducted as a subsurface structure survey in Concepción. The S‐wave velocity profiles were estimated from the inversion of the Rayleigh‐wave phase velocity and the horizontal‐to‐vertical ratio. The different spectral characteristics of the records at CONC and CCSP could be explained by the theoretical amplification factors computed from the velocity profiles. Further studies on seismic microzoning of the city with an emphasis on the subsurface structure should improve disaster planning in Concepción.