Abstract: In order to study the effect of absorption of doping on the defect mode of photonic crystal,complex refractive index and matrix methods have been used to analyze the change of defect mode's peak transmissivity and its full width while the changes of the extinction coefficient and doping thickness take place.It has been found that with the increase of the extinction coefficient,the defect mode's peak transmissivity will decrease gradually and the FWHM will increase and their speed of increase and decrease will be different. When the extinction coefficient is constant,with the increase of the thickness of doping,the defect mode's peak transmissivity and the FWHM will decrease correspondingly.Therefore the effect of the absorption of dopant on the defect mode should be taken into account for the design of phonic crystal device.