Dependent component analysis (DCA) was applied to directly estimate source spectral profiles from IR spectra of synthetic mixtures and characterize processing batch for preparation of radix scutellariae. The results show that DCA can estimate information of dependent components (DCs) from the measured infrared spectral (IR) signal obtained during the processing batch for preparation of radix scutellariae, and the estimated information of DCs is corresponding to the IR features of the active components of scutelliare; by inspection of the change trends of the estimated DCs, the endpoint of the processing batch was determined as 55 min. The proposed approach provides a novel way for process analysis and endpoint determination of procedure for preparation of scutellariae.