To improve the detection capability of pulsed thermography (PT), factor analysis algorithm was applied to image sequence processing in pulsed infrared thermographic nondestructive examination(NDT). The principle of factor analysis was introduced and the procedure of image sequence processing and reconstruction was described. In order to illustrate the validity of this method, a glass fiber reinforced plastic sample with artificial internal defects was tested by PT. It is shown that the common factor images can be used to improve the recognition of flaws; factor analysis is more flexible than principal component analysis (PCA); the reconstructed image sequence can improve the defect’s signal to noise ratio(SNR) and decrease the nonuniform heating effect, thus the detection capability of PT is enhanced.