Objective To explore the clinical characteristics and influencing factors for prognosis of patients with bloodstream infection (BSI) caused by Stenotrophomonas maltophilia (S. maltophilia). Methods Clinical data of patients with S. maltophilia BSI in Liuzhou People’s Hospital from January 2019 to December 2023 were retrospectively analyzed. Patients were divided into good prognosis group and poor prognosis group according to their prognosis. Risk factors for poor prognosis were analyzed by univariate analysis and binary logistic regression analysis. Results From 2019 to 2023, a total of 36 patients were diagnosed with S. maltophilia BSI, with an average age of (51.8±22.6) years. The most common clinical symptom was fever (91.7%), followed by respiratory symptoms (25.0%). 33 patients (91.7%) had underlying diseases, 31 patients (86.1%) had healthcare-associated infection, and 23 patients (63.9%) underwent invasive procedures before onset. Among the 36 patients with S. maltophilia BSI, 12 (33.3%) had a poor prognosis. Univariate analysis showed that underlying blood diseases, length of hospital stay ≥30 days, agranulocytosis, and elevation of C-reactive protein (CRP) were related to poor prognosis of patients with S. maltophilia BSI (all P<0.05). Binary logistic regression analysis results showed that underlying blood diseases, length of hospital stay ≥30 days, and agranulocytosis were independent risk factors for poor prognosis in patients (all P<0.05). Conclusion Patients with S. maltophilia BSI are critically ill with high mortality. Underlying blood diseases, length of hospital stay ≥30 days, and agranulocytosis are independent risk factors for poor prognosis in patients.