The present data are subsurface velocity structures retrieved by applying the theory of diffuse field concept to the strong motion data of earthquakes observed at 1744 sites of K-NET and KiK-net (operated by the National Institute of Earth Science and Disaster Resilience) in Japan. Additionally, the data include peak fundamental and predominant frequencies as identified from the observed and theoretical horizontal-to-vertical spectral ratios for earthquakes (eHVSR). Based on our novel proposed quarter wavelength approach, we could define the effective bedrock depths and correlate them with the corresponding peak frequencies. For better usefulness of the present data, we classify the sites into four categories based on the correlation coefficients and residuals between the observed and theoretical eHVSR. The potentiality of these data could be reused by other researchers to develop new approaches related to the limitations of the established bedrock regressions and the uncertainty associated with the retrieved subsurface velocity structures, particularly at sites with low correlation coefficients and high residuals. Moreover, the data of the subsurface velocity structures could be reused as initial models for future microtremor applications and better enhance the retrieved velocity structures and the associated theoretical eHVSR curves. The data of the present paper is associated with original published article by Thabet et al. [1], which is presented in the Soil Dynamics and Earthquake Engineering under the title “A computational approach for bedrock regressions with diffuse field concept beneath the Japan Islands” [1].