Large Language Models (LLMs) struggle with accuracy, domain-specific reasoning, and interpretability in vertical domains. Traditional preference alignment methods like Reinforcement Learning from Human Feedback (RLHF) and Direct Preference Optimization (DPO) often overlook the underlying knowledge sources and reasoning logic. This paper introduces RACE-Align (Retrieval-Augmented and Chain-of-Thought Enhanced Alignment), a novel framework designed to address these limitations. RACE-Align systematically constructs a binary preference dataset incorporating external knowledge support and explicit Chain-of-Thought (CoT) reasoning, then aligns LLMs using the DPO algorithm. The core innovation lies in its preference data construction strategy: it integrates AI-driven retrieval for factual grounding, enhancing knowledgeability and accuracy, and emphasizes the optimization of domain-specific CoT, treating the reasoning process itself as a key preference dimension. A multi-stage, AI-driven refinement pipeline cost-effectively generates these preference pairs. Experimental validation in Traditional Chinese Medicine (TCM) using Qwen3-1.7B as the base model demonstrates that RACE-Align significantly outperforms the original base model and a model fine-tuned only with Supervised Fine-Tuning (SFT). Improvements were observed across multiple dimensions, including answer accuracy, information richness, application of TCM thinking patterns, logicality and depth of reasoning, and interpretability. These findings suggest RACE-Align offers an effective pathway to enhance LLMs' knowledge application, reasoning reliability, and process transparency in complex vertical domains.