The constructive and destructive fringe due to etaloning effects is an universal phenomenon emerging in the imaging system using the back-illuminated CCD. An adaptive method based on the bi-dimensional empirical mode decomposition (BEMD) and principal component analysis (PCA) was proposed to suppress the nonlinear fringe in interference imaging spectrometer. The feasibility was verified by reconstructing the fringe and interferogram taken by interference imaging spectrometer effectively. Meanwhile, the vertical CCD mosaic stripes was suppressed obviously. Comparing the retrieved contaminated and corrected spectrums, it was found that the sidelobes introduced by the nonlinear background was removed. It provides us a time-saving, without prior knowledge, and automatic approach for defringing.