The objective of this study is to investigate in detail the characteristics of strong ground motions separated from acceleration Fourier spectra of ground motions observed by K‐NET, KiK‐net, and the Japan Meteorological Agency (JMA) Shindokei network in Japan using the generalized spectral inversion method. The separation method used here is the same as that proposed by Kawase and Matsuo (2004), with the same reference bedrock site at YMGH01. We include events with magnitude equal to or larger than 4.5 observed from 1996 to 2011. Our results are in good agreement with previous results regarding source, path, and site characteristics, but with higher stability thanks to the increased amount of data. We obtain site amplification factors common to all source types but with different Q‐values for three source categories: crustal earthquakes (type C), subducting plate‐boundary earthquakes (type B), and intraplate earthquakes (type I). We find that our frequency‐dependent Q‐values are comparable to those of previous studies, and that the obtained Q‐values depend on the traveling regions. As for the geometric spreading factor n, we find that for type B and type I earthquakes, the value is close to 1.0 as expected, but type C earthquakes show apparent frequency dependence. From the corner frequencies of source spectra, we calculate Brune’s stress parameters and find a clear magnitude dependence, in which smaller events tend to spread over a wider range while maintaining the same maximum value. This means that stress drops for larger events would be maximal. We confirm that this is exactly the case for several mainshock–aftershock sequences. The average stress parameters are 5.1 and 6.0 MPa for types B and I, and 0.8 MPa for type C. This large difference between types B and I and type C can be explained primarily by the depth dependence of stress parameters.