Large horizontal ground motions with peak ground accelerations (PGAs) of more than 800  cm/s2 and peak ground velocities of nearly 60  cm/s were observed at a KiK‐net station, Iwase (IBRH11), during the 2011 Mw 9.0 Tohoku, Japan, earthquake. We investigated site effects on the large ground motions by inverting the subsurface structure and simulating ground motions considering soil nonlinearity. The structure from the seismic bedrock to the surface in the linear regime was inverted from (1) array records of microtremors using Rayleigh‐wave inversion, (2) surface‐to‐borehole spectral ratios of weak motions using S‐wave inversion based on the 1D wave propagation theory, and (3) horizontal‐to‐vertical spectral ratios of weak motions using the inversion based on the diffuse‐field theory for plane waves. The main cause of the large ground motions was found to be a strong impedance contrast between soft layers with an S‐wave velocity (VS) of less than 381  m/s and a layer with VS=2371  m/s at a depth of 30 m. The strong motions at the surface during the 2011 Tohoku earthquake simulated by equivalent‐linear analysis using borehole records at a depth of 103 m are in reasonable agreement with the observed records, whereas those simulated using linear analysis were approximately twice as large as the observed values. The results showed that the nonlinearity of the surface soils reduced the amplification factors and the PGAs by half compared with the values for the linear regime. The PGAs of the bedrock motions with VS=2371  m/s were estimated, using equivalent‐linear analysis, to have reached approximately 500  cm/s2.