Objective: Large Language Models (LLMs) demonstrate significant capabilities in medical text understanding and generation. However, their diagnostic reliability in complex clinical scenarios remains limited. This study aims to enhance LLMs' diagnostic accuracy and clinical reasoning ability. Method: We propose an Etiology-Aware Attention Steering Framework to integrate structured clinical reasoning into LLM-based diagnosis. Specifically, we first construct Clinical Reasoning Scaffolding (CRS) based on authoritative clinical guidelines for three representative acute abdominal emergencies: acute appendicitis, acute pancreatitis, and acute cholecystitis. Next, we develop the Etiology-Aware Head Identification algorithm to pinpoint attention heads crucial for the model's etiology reasoning. To ensure reliable clinical reasoning alignment, we introduce the Reasoning-Guided Parameter-Efficient Fine-tuning that embeds etiological reasoning cues into input representations and steers the selected Etiology-Aware Heads toward critical information through a Reasoning-Guided Loss function. Result: On the Consistent Diagnosis Cohort, our framework improves average diagnostic accuracy by 15.65% and boosts the average Reasoning Focus Score by 31.6% over baselines. External validation on the Discrepant Diagnosis Cohort further confirms its effectiveness in enhancing diagnostic accuracy. Further assessments via Reasoning Attention Frequency indicate that our models exhibit enhanced reliability when faced with real-world complex scenarios. Conclusion: This study presents a practical and effective approach to enhance clinical reasoning in LLM-based diagnosis. By aligning model attention with structured CRS, the proposed framework offers a promising paradigm for building more interpretable and reliable AI diagnostic systems in complex clinical settings.