While reinforcement learning-trained Large Reasoning Models (LRMs, e.g., Deepseek-R1) demonstrate advanced reasoning capabilities in the evolving Large Language Models (LLMs) domain, their susceptibility to security threats remains a critical vulnerability. This weakness is particularly evident in Chain-of-Thought (CoT) generation processes, where adversarial methods like backdoor prompt attacks can systematically subvert the model's core reasoning mechanisms. The emerging Chain-of-Thought Attack (CoTA) reveals this vulnerability through exploiting prompt controllability, simultaneously degrading both CoT safety and task performance with low-cost interventions. To address this compounded security-performance vulnerability, we propose Thought Purity (TP): a defense paradigm that systematically strengthens resistance to malicious content while preserving operational efficacy. Our solution achieves this through three synergistic components: (1) a safety-optimized data processing pipeline (2) reinforcement learning-enhanced rule constraints (3) adaptive monitoring metrics. Our approach establishes the first comprehensive defense mechanism against CoTA vulnerabilities in reinforcement learning-aligned reasoning systems, significantly advancing the security-functionality equilibrium for next-generation AI architectures.