Medication recommendations seek to deliver personalized drug combinations based on patients' clinical information, where ensuring transparent decision-making and personalized safety are of paramount importance. However, existing approaches predominantly operate as ''black boxes'', offering limited interpretability and hindering clinician trust. Furthermore, they typically rely on fixed, patient-agnostic safety constraints, neglecting the heterogeneity of risk tolerance across individuals, which poses significant risks to vulnerable populations. To address these gaps, we propose RES-MR, a novel Risk-aware Reasoning framework for Explainable and Safe Medication Recommendation using LLMs. RES-MR follows a two-stage training paradigm: (1) an explainable clinical reasoning distillation stage to elicit diagnostic capabilities by fine-tuning on synthesized reasoning trajectories, grounded in patient-specific knowledge from graph retrieval; and (2) a risk-aware policy optimization stage to dynamically balance therapeutic efficacy with personalized safety. This stage employs disentangled drug factors to construct patient-specific reference prototypes that capture desired therapeutic drug features and risk features to avoid. These prototypes enable risk boundary calibration and guide the model toward safe recommendations via reward shaping and clipping. Extensive experiments on benchmark datasets demonstrate that RES-MR significantly outperforms state-of-the-art baselines in terms of accuracy, safety, and explainability. Our code and data are available at: https://github.com/wangcong2001/RES-MR.