Non-destructive metrology is essential for quality control in semiconductor manufacturing, yet conventional techniques face limitations in characterizing epitaxial silicon-germanium films. This study introduces second harmonic generation (SHG) as a novel approach to address two critical challenges in SiGe process monitoring. First, we demonstrate that SHG can effectively characterize lattice symmetry and defect states in SiGe thin films, enabling discrimination of the effects of different pre-cleaning methods during growth. These findings are supported by destructive measurements and electrical tests of Metal-Oxide-Semiconductor devices. Secondly, we show that SHG can accurately determine the germanium ratio of ultrathin SiGe films—overcoming the limitations of conventional techniques such as X-ray photoelectron spectroscopy, which suffers from substrate interference. Our findings offer a powerful, non-destructive solution for in-line metrology, with significant potential to optimize next-generation semiconductor fabrication processes.