Bash script comprehension is a significant challenge in Linux environments due to Bash’s syntactic freedom and complex command structures. Despite its critical role in system administration and development, Bash scripts often lack adequate comments, hindering code readability and maintainability. Existing approaches to automated Bash comment generation face two main challenges: (1) Limited training datasets that inadequately represent real-world Bash usage patterns, particularly for complex multi-line scripts; and (2) Insufficient understanding of Bash-specific concepts by Large Language Models (LLMs). Our empirical analysis shows that even after standard training, LLMs still struggle to precisely understand complex Bash command semantics, leading to inaccurate comments. To address these challenges, we propose Bash-Commenter, an advanced comment generation method based on LLaMA-3.1-8B that employs a three-stage pipeline. First, we perform Continual Pre-training (CPT) on large-scale Bash script data to enhance the model’s foundational understanding of Bash syntax and semantics, addressing the second challenge. Second, to overcome data limitations (the first challenge), we construct a comprehensive dataset of complex, multi-line scripts and then perform Supervised Fine-tuning (SFT). Finally, to resolve the subtle semantic errors that persist, we introduce Syntax-Aware Preference Optimization (SAPO). This method automatically constructs preference pairs by applying single, atomic operations (e.g., modifying a command option or removing an argument) to a script’s Abstract Syntax Tree (AST), creating minimal pairs of correct and subtly incorrect scripts. This final optimization stage enables fine-grained command semantics learning and context-dependent quality assessment, significantly improving comment accuracy. We evaluate Bash-Commenter on single-line Bash commands and multi-line Bash scripts. Our method outperforms state-of-the-art baselines, achieving 33.40% BLEU-4, 58.26% METEOR, and 57.03% ROUGE-L for 1,064 single-line commands, and 22.15% BLEU-4, 43.89% METEOR, and 32.80% ROUGE-L for 1,046 multi-line scripts. Moreover, human evaluation demonstrates the superior quality of comments generated by Bash-Commenter in terms of correctness, completeness, and naturalness.