The kinematic source rupture process of the 2004 Chuetsu, mid-Niigata prefecture, Japan, earthquake, is estimated from strong-motion data by the linear waveform inversion method. In order to develop appropriate Green’s functions, one-dimensional velocity structure models for each station are constructed by modeling the aftershock waveforms. The estimated top of the bedrock is deeper at the western side of the fault and relatively shallow at the eastern side. This tendency coincides with other investigations of seismic tomography and microtremor array observations. The obtained source model shows large slips in the vicinity of the hypocenter. The reverse slipping rupture originated from the deeper part of the fault and propagated toward the up-dip and southwest directions. The near-surface slip is small. Two tests are demonstrated to check the stability of the obtained source model. The first test examines the effects of the number of available stations on the solution, and the second test examines how the difference in the target waveform type affects the solution. The number of stations affects the variation of slip amount, and more than 12 stations appear to be sufficient to obtain a stable solution in this case. The difference in the target wave type in the data set does not significantly affect the solution if the number of stations is sufficient and the Green’s functions are well calibrated. The model obtained using calibrated velocity structure models shows clear image of high-slip area compared to the model obtained using a single velocity structure model.