The invention discloses window-scanning thermal imaging defect detecting and tomography method and system. When the system works, a detected objected is scanned by a heat source and a thermal imager at fixed speed and is heated by the heat source, and temperature information varied along the time after the surface of the detected objected is heated is recorded by the thermal imager as original data; the original data is reconstructed to acquire a temperature variation sequence of each point of the detected objected as a detection signal; a specific signal is utilized or produced as a reference signal; the detection signal and the reference signal are processed by virtue of methods such as time domain, frequency domain and mutual correlation; a time domain feature value, a frequency domain feature value, a mutual correlation amplitude feature value and a mutual correlation phase feature value are extracted, and therefore, the defect detection and the tomography are achieved. The method and the system can be applied to the nondestructive testing of devices, the characterization assessment of materials and the quality control of products in the fields of aerospace, new materials, petrochemical engineering, nuclear power, railways, automobiles, special equipment, machinery, metallurgy and civil construction.