Micro-defects inside metal matrix composite structure seriously influence the mechanic properties of materials and can undermine machine operations. In order to detect the micro-defects, we can make use of one of the nonlinear acoustic features, i.e., harmonics, which usually appear together with ultrasound when propagating through a damaged material. Based on the relationship between the harmonics, a method of using nonlinear acoustic harmonic amplitude ratio to distinguish micro-defects in metal matrix composite structure is discussed. The test results show that acoustic features, such as second harmonic excitation efficiency were very obvious for the damaged group samples. The method presented is effective in detecting the micro-defects, which means that nonlinear acoustic waves may provide us a good solution for quantitative evaluation of the early damages in metal matrix composite structure.