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Surface crack detection and sizing is essential for the manufacturing and maintenance of engines, run parts, and other metal elements of aircrafts. Among various non-destructive detection methods, the fully non-contact and non-intrusive technique based on laser-stimulated lock-in thermography (LLT) has recently attracted a lot of attention from the aerospace industry. We propose and demonstrate a system of reconfigurable LLT for three-dimensional surface crack detection in metal alloys. For large area inspection, the multi-spot LLT can speed up the inspection time by a factor of the number of spots. The minimum resolved size of micro-holes is ~50 µm in diameter limited by the magnification of the camera lens. We also study the crack length ranging from 0.8 to 3.4 mm by varying the modulation frequency of LLT. An empirical parameter related to the thermal diffusion length is found to show the linear dependence with the crack length. With the proper calibration, this parameter can be used to predict the sizing of the surface fatigue cracks. Reconfigurable LLT allows us to quickly locate the crack position and accurately measure its dimensions. This method is also applicable to the non-destructive detection of surface or sub-surface defect in other materials used in various industries.