Nonlinearity of damaged materials is often assumed to be correlated with the cumulative length of micro-cracks discounting the influence of crack width and roughness. To investigate the influence of microstructural features of realistic cracks on the nonlinear elastic properties, Dynamic Acousto-Elastic Testing (DAET) is performed on two aluminum alloy samples (30 × 40 × 170 mm3) with a single fatigue-crack. The cracks on the two samples are of similar length but have dissimilar microstructural features due to the different stress intensity factors used during the fatigue tests. DAET is carried out with a surface wave probe to measure the near-surface nonlinearity at a number of locations along each crack. The geometric features of the cracks, including crack width and roughness, are extracted from a series of scanning electron microscope images. DAET results demonstrate that nonlinearity varies along the crack; both samples exhibit greater nonlinearity near the notch, where the crack is wider than near the crack tip. However, the nonlinearity parameters obtained from the sample with a smoother crack are one order of magnitude larger than those of the sample with a relatively rough crack. In addition, the nonlinearity signatures of the two cracks exhibit very different tension/compression asymmetry. This study provides valuable data that not only directly correlates the nonlinear ultrasonic signatures and crack interface features but also illuminates the micro-mechanisms and origins of the measured nonlinearities.