The peak localization of axial response signal (ARS) is essential for height extraction in confocal microscopy. In previous evaluations about peak localization, an aberration-free confocal system was Savegenerally analyzed by taking the comprehensive effects of random noise and sample surface height into consideration. In this paper, the combined influence of optical aberration, random noise and sample surface height on peak extraction are evaluated using Monte Carlo simulations. At first, a certain amount of optical aberration is added into the ARS model. Then the systematic peak extraction error and standard deviation are analyzed. In the end, comparisons are provided between an aberration-free and an aberrated confocal system. Our simulations demonstrate that optical aberration is a critical influencing factor in peak extraction computation in terms of both accuracy and precision. More specifically, aberration-induced asymmetry of ARS that exceeds certain limits will result in a tremendous increase in systematic peak extraction error and standard deviation. Our developed metric “degree of asymmetry” can offer a reference for determining the aberration tolerance in confocal metrology and acting as guides for further performance enhancement of confocal microscopy.