Preference-based reinforcement learning (PbRL) stands out by utilizing human preferences as a direct reward signal, eliminating the need for intricate reward engineering. However, despite its potential, traditional PbRL methods are often constrained by the indistinguishability of segments, which impedes the learning process. In this paper, we introduce Skill-Enhanced Preference Optimization Algorithm (S-EPOA), which addresses the segment indistinguishability issue by integrating skill mechanisms into the preference learning framework. Specifically, we first conduct the unsupervised pretraining to learn useful skills. Then, we propose a novel query selection mechanism to balance the information gain and distinguishability over the learned skill space. Experimental results on a range of tasks, including robotic manipulation and locomotion, demonstrate that S-EPOA significantly outperforms conventional PbRL methods in terms of both robustness and learning efficiency. The results highlight the effectiveness of skill-driven learning in overcoming the challenges posed by segment indistinguishability.