As a high quality seismic imaging method, full waveform inversion (FWI) can accurately reconstruct the physical parameter model for the subsurface medium. However, application of the FWI in seismic data processing is computationally expensive, especially for the three-dimension complex medium inversion. Introducing blended source technology into the frequency-domain FWI can greatly reduce the computational burden and improve the efficiency of the inversion. However, this method has two issues: first, crosstalk noise is caused by interference between the sources involved in the encoding, resulting in an inversion result with some artifacts; second, it is more sensitive to ambient noise compared to conventional FWI, therefore noisy data results in a poor inversion. This paper introduces a frequency-group encoding method to suppress crosstalk noise, and presents a frequency- domain auto-adapting FWI based on source-encoding technology. The conventional FWI method and source-encoding based FWI method are combined using an auto-adapting mechanism. This improvement can both guarantee the quality of the inversion result and maximize the inversion efficiency.