Gears’ surface morphology changes over time due to wear and contact fatigue, impacting their performance. The ISO Geometrical Product Specifications 21920 standard lists up to 60 surface roughness parameters to help characterize this evolution. However, selecting the most effective parameters for gear surface morphology remains challenging. This paper presents a method for selecting roughness parameters to analyze gear surface morphology evolution, focusing on tooth surface characterization and damage identification in FZG gear tests. Using a profilometer, the tooth surface morphology was measured during micro-pitting tests. The orthogonal distance fitting algorithm were employed to determine tooth profile deviations before and after testing. A cross-correlation algorithm aligned profiles to assess changes at each test stage, while a cubic spline low-pass filter extracted tooth surface roughness profiles. Key roughness parameters—Including Ra, Rq, Rsk, and Rku were calculated and analyzed, revealing their effectiveness in reflecting micro-wear and micro-pitting damage. The method optimizes parameter selection for comprehensive characterization of tooth surface morphology evolution, minimizing redundancy in calculations.