Site resonance frequency is a crucial parameter for estimating site effects. However, there is currently no consensus on how to identify the bedrock interface to obtain the site resonance frequency. In this study, we identified 43 stations that can be regarded as one‐dimensional sites from the KiK‐net network in Japan, which consists of 699 stations. By analyzing the horizontal‐to‐vertical spectral ratio and surface‐to‐borehole spectral ratio of strong motion observation recordings, the fundamental resonance frequency (f0) of these 43 sites was determined. Subsequently, the correlation between the f0 values obtained from theoretical noise horizontal‐to‐vertical spectral ratio (NHV) with different bedrock interfaces and the f0 values determined from observation was analyzed. The conclusion shows that the f0 is primarily influenced by shallow interfaces with high S‐wave impedance contrasts (ICs). Specifically, when the bedrock interface is taken as the interface with ICs greater than 2.5 that appears for the first time, or the interface with ICs greater than 1.5 that appears for the second time, there is a strong correlation (greater than 0.86) between the f0 values obtained from theoretical NHV and from observation. These findings can provide a quantitative reference for accurately determining the fundamental resonance frequency.