Current safety alignment techniques for large language models (LLMs) face two key challenges: (1) under-generalization, which leaves models vulnerable to novel jailbreak attacks, and (2) over-alignment, which leads to the excessive refusal of benign instructions. Our preliminary investigation reveals semantic overlap between jailbreak/harmful queries and normal prompts in embedding space, suggesting that more effective safety alignment requires a deeper semantic understanding. This motivates us to incorporate safety-policy-driven reasoning into the alignment process. To this end, we propose the Safety-oriented Reasoning Optimization Framework (SaRO), which consists of two stages: (1) Reasoning-style Warmup (RW) that enables LLMs to internalize long-chain reasoning through supervised fine-tuning, and (2) Safety-oriented Reasoning Process Optimization (SRPO) that promotes safety reflection via direct preference optimization (DPO). Extensive experiments demonstrate the superiority of SaRO over traditional alignment methods.