The invention discloses a full waveform inversion method and a system based on logging data constraints. The method comprises steps: Land seismic data are used for building an initial velocity field of a seismic profile; according to known logging data, a logging model based on the logging information is built; based on the initial velocity field and the logging model, a comprehensive interpolation model for the seismic profile is built; inversion calculation is carried out on the comprehensive interpolation model, the comprehensive interpolation model is updated according to data residual between calculation data and the land seismic data, and thus, a full waveform inversion model in a condition of missing of low frequency information in the initial velocity field is determined. The full waveform inversion modeling precision is improved, dependence on the seismic low frequency data by the full waveform inversion is reduced, and a full waveform inversion process for land lowest available frequency band data can be completed.