Small sample sizes cause epistemic uncertainties in reliability estimation and even result in potential risks in maintenance strategies. To explore the difference between stochastic- and uncertain-process-based degradation modeling in reliability estimation for small samples, this study proposes a comparative analysis methodology based on the range of quantile reliable lifetime (RQRL). First, considering both unit-to-unit variability and epistemic uncertainty, we proposed the Wiener and Liu process degradation models. Second, based on the RQRL, a comparative analysis method of different degradation models for reliability estimation under various sample sizes and measurement times was proposed. Third, based on a case study, the sensitivities of the Wiener and Liu process degradation models for various sample sizes and measurement times were compared and analyzed based on the RQRL. The results demonstrated that using the uncertain process degradation model improved the uniformity and stability of reliability estimation under small-sample conditions.