The emergence of Chain-of-Thought (CoT) has established a robust foundation for Large Reasoning Models (LRMs). While deep reasoning is widely believed to enhance safety alignment, the stability of alignment mechanisms under extended reasoning remains underexplored. This paper challenges the prevailing view by revealing a critical vulnerability: Deep Reasoning May Induce Alignment Collapse. To rigorously quantify this phenomenon, we propose the Alignment Loss Rate (ALR) metric. Our experiments demonstrate that as reasoning depth increases, ALR rises significantly, indicating a severe degradation in model robustness against external perturbations. Capitalizing on this instability, a novel jailbreaking paradigm, Reasoning Trap (RT), is proposed. RT induces the model into extended reasoning to amplify the impact of adversarial attacks, leading to a sharp decline in safety capabilities. To elucidate the mechanism behind this collapse, we identify Attention Dilution as the root cause, arising from the competition for attention between the extended reasoning process and the original input. To mitigate this, Reasoning Residual Alignment (RRA), a lightweight defense strategy that dynamically re-emphasizes the input via residual connections integrated with the reasoning process.
Large Reasoning Models (LRMs) exhibit strong problem-solving abilities, yet their safety alignment often degrades when handling harmful queries. Existing approaches to improving safety largely rely on additional training or preference optimization, while offering limited understanding of the internal mechanisms behind safety failures. In this work, we investigate this failure through a token-level positional analysis of refusal dynamics and identify a localized vulnerability at the onset of reasoning, which we term Onset Refusal Collapse (ORC). We find that the refusal-related signal of LRMs drops sharply at the first generated token under harmful queries, which is associated with unsafe response generation. Motivated by this finding, we propose SafeToken, a lightweight inference-time intervention that injects a learned continuous safety anchor precisely at reasoning onset. Despite updating only a single token embedding, SafeToken effectively mitigates ORC, improves safety on harmful-query benchmarks, and largely preserves reasoning utility. These results suggest that safety failures in LRMs can arise from a transient breakdown at the critical transition from understanding to generation.
Large reasoning models (LRMs) achieve strong performance on complex reasoning tasks but often generate harmful responses to malicious user queries. This paper investigates the underlying cause of these safety risks and shows that the issue lies in the reasoning structure itself. Based on this insight, we claim that effective safety alignment can be achieved by altering the reasoning structure. We propose AltTrain, a simple yet effective post training method that explicitly alters the reasoning structure of LRMs. AltTrain is both practical and generalizable, requiring no complex reinforcement learning (RL) training or reward design, only supervised finetuning (SFT) with a lightweight 1K training examples. Experiments across LRM backbones and model sizes demonstrate strong safety alignment, along with robust generalization across reasoning, QA, summarization, and multilingual setting.
Large Reasoning Models (LRMs) pose a dual-surface safety challenge: both intermediate reasoning traces and final answers can contain harmful content. Existing alignment methods often operate at the whole-response level, allowing unsafe reasoning to be masked by a safe-looking final answer. We propose Segment-aware Listwise Target DPO (SaLT-DPO), which addresses this gap through three mechanisms: (1) segment-aware listwise alignment that decomposes responses into reasoning and answer segments, independently scores each segment's safety, and aligns length-normalized segment rewards with soft target distributions over multiple candidates; (2) joint safety coherence regularization that applies a weakest-link principle to promote safety consistency across both segments; and (3) utility anchoring on benign prompts to mitigate over-refusal and reasoning degradation. Experiments on three LRMs show that SaLT-DPO consistently reduces unsafe rates for both reasoning and answer segments while mitigating degradation in benign compliance and preserving general reasoning performance. Ablation studies demonstrate the complementary contributions of its components.