Eddy Current Pulsed Thermography (ECPT), an emerging Non-Destructive Testing and Evaluation technique, has been applied for a wide range of materials. The lateral heat diffusion leads to decreasing of temperature contrast between defect and defect-free area. To enhance the flaw contrast, different statistical methods, such as Principal Component Analysis and Independent Component Analysis, have been proposed for thermography image sequences processing in recent years. However, there is lack of direct and detailed independent comparisons in both algorithm implementations. The aim of this article is to compare the two methods and to determine the optimized technique for flaw contrast enhancement in ECPT data. Verification experiments are conducted on artificial and thermal fatigue nature crack detection.