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Current research primarily emphasizes boosting LLMs' performance on scientific QA benchmarks by training on larger, more comprehensive datasets with extended reasoning chains. However, these approaches neglect the essence of the scientific reasoning process -- logicality, which is the rational foundation to ensure the validity of reasoning steps leading to reliable conclusions. In this work, we make the first systematic investigation into the internal logicality underlying LLM scientific reasoning, and develop a scientific logicality-enriched methodology, including a set of assessment criteria and data sampling methods for logicality-guided training, to improve the logical faithfulness as well as task performance. 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