Ultrafast ultrasonic techniques using picosecond/femtosecond lasers show promise for the nondestructive evaluation at fine spatial resolutions because the induced ultrasonic waves have an extremely high frequency range, from GHz to THz. However, most existing applications are based on the linear feature variation of the measured ultrafast ultrasonic waves; this is limited by the linearity assumptions in lock-in detection schemes adopted for ultrafast ultrasonic measurement. This study proposes a technique to measure ultrafast nonlinear ultrasonic waves using a femtosecond laser and a modified lock-in detection scheme. The advantages of the proposed technique are as follows. (1) The developed technique can measure nonlinear ultrasonic waves induced by a femtosecond laser; (2) linear and nonlinear ultrasonic responses can be decomposed and measured using a modified lock-in detection scheme; and (3) the decomposed nonlinear ultrasonic waves can be used for effective micro defect detection and microstructure characterization at sub-micrometer scale. The proposed technique was used to successfully perform validation tests on micro crack detection in a silicon wafer and microstructure characterization of an additively manufactured Ti-6Al-4V sample.