Large reasoning models (LRMs) show strong capabilities in complex reasoning, yet their marginal gains on evidence-dependent factual questions are limited. We find this limitation is partially attributable to a reasoning–answer hit gap, where the model identifies the correct facts during reasoning but fails to incorporate them into the final response, thereby reducing factual fidelity. To address this issue, we propose MR-ALIGN, a Meta-Reasoning informed alignment framework that enhances factuality without relying on external verifiers. MR-ALIGN quantifies state-transition probabilities along the model’s thinking process and constructs a transition-aware implicit reward that reinforces beneficial reasoning patterns while suppressing defective ones at the atomic thinking segments. This re-weighting reshapes token-level signals into probability-aware segment scores, encouraging coherent reasoning trajectories that are more conducive to factual correctness. Empirical evaluations across four factual QA datasets and one long-form factuality benchmark show that MR-ALIGN consistently improves accuracy and truthfulness while reducing misleading reasoning. These results highlight that aligning the reasoning process itself, rather than merely the outputs, is pivotal for advancing factuality in LRMs.

Large language models (LLMs) often generate convincing, fluent explanations. However, different from humans, they often generate inconsistent explanations on different inputs. For example, an LLM may explain “all birds can fly” when answering the question “Can sparrows fly?” but meanwhile answer “no” to the related question “Can penguins fly?”. Explanations should be consistent across related examples so that they allow humans to simulate the LLM’s decision process on multiple examples. We propose explanation-consistency finetuning (EC-finetuning), a method that adapts LLMs to generate more consistent natural-language explanations on related examples. EC-finetuning involves finetuning LLMs on synthetic data that is carefully constructed to contain consistent explanations. Across a variety of question-answering datasets in various domains, EC-finetuning yields a 10.0% relative explanation consistency improvement on 4 finetuning datasets, and generalizes to 7 out-of-distribution datasets not seen during finetuning (+4.5% relative). We will make our code available for reproducibility.