Background Leptospirosis is a global zoonotic infection. Severe leptospirosis typically manifests as Weil’s syndrome with jaundice and acute kidney injury, while isolated diffuse alveolar hemorrhage (DAH) without jaundice or acute kidney injury (the classic features of Weil’s syndrome) is rare and easily misdiagnosed. Traditional diagnostic methods have notable limitations in the acute phase of infection, and the diagnostic value of metagenomic next-generation sequencing (mNGS) for atypical leptospirosis remains insufficiently characterized. This report highlights the clinical novelty of this rare phenotype and the diagnostic value of mNGS. Case presentation A 60-year-old male farmer was admitted with 6 days of fever and 2 days of progressive chest tightness, with a history of contaminated water exposure via broken skin before symptom onset. Initial chest computed tomography showed bilateral pulmonary infiltrates, and he was misdiagnosed with severe community-acquired pneumonia and acute respiratory failure. Despite empiric broad-spectrum anti-infective therapy, his condition progressed rapidly, requiring invasive mechanical ventilation. Bronchoalveolar lavage fluid mNGS identified Leptospira spp., and the diagnosis was revised to leptospirosis with isolated DAH. After targeted anti-infective therapy combined with methylprednisolone pulse therapy, his respiratory function improved rapidly. He was weaned from mechanical ventilation on day 7 of admission, discharged with complete symptom resolution on day 19, and had no sequelae at 25-day follow-up. Conclusion This case highlights that leptospirosis can present with isolated DAH as the sole severe manifestation without classic hepatorenal impairment, requiring high clinical suspicion in endemic areas. Bronchoalveolar lavage fluid mNGS may be a valuable tool for rapid diagnosis of atypical leptospirosis, which may reduce misdiagnosis and contribute to improved clinical outcomes.