Traditional methods to characterize material deterioration of asphalt mixture are typically destructive to the local integrity of the inspected structure, which is therefore not suitable for the large-scale assessment in an efficient fashion. In this paper, an ultrasonic nondestructive evaluation (NDE) method based on the principle of second harmonic generation (SHG) of Rayleigh surface waves is proposed to apply for the quantitation of cracking variation of asphalt specimens subjected to the fracture-healing cycles. The nonlinear parameter which is the relative amplitude of second harmonic is used to caliber the crack growing in the loading tests and crack healing under the elevated temperature. The feasibility of SHG technique in the crack characterization is justified by the excellent correlation of nonlinear parameter with the crack development corresponding to the fracture force and the crack shrinkage corresponding to the rising temperature. The sensitivity of SHG technique to the crack variation is further demonstrated through a comparison with width measurements from the crack detector. The SHG measurements present an alteration of orders of magnitude with respect to the alternative change of crack. Particularly the SHG measurement demonstrates an excellent capability to distinguish the tiny cracks after the first three healing cycles, compared to the zero reading of crack detector. The findings in this work indicate that the SHG technique is a potentially viable and robust method to characterize microstructural variation of asphalt mixture.