This study conducted an initial experimental investigation to compare the performance of the charge comparison (CC) and constant fraction time-over-threshold (CF-TOT) methods under various operating conditions. In this study, the influence of overvoltage exhibited tendencies according to the method used, though generally, a high overvoltage did not guarantee superior performance in pulse shape discrimination (PSD). Moreover, the results of the CC method consistently demonstrated PSD performance irrespective of operating conditions, including apparatus configuration, operating voltage, and temperature. Conversely, the CF-TOT method showed significant improvement, particularly in the low electron equivalent region, by employing external equipment or controlling the experimental conditions to mitigate noise factors. We believe that this research will not only contribute to enhancing particle classification performance under low-temperature conditions by proposing the utilization of the CF-TOT method but will also facilitate the optimization of SiPM-based systems for PSD.