Objective COVID-19 is becoming a global pandemic and often develops extrapulmonary organ injury. However, the risk factors for extrapulmonary organ injury are still unclear. We aim to explore the risk factors for extrapulmonary organ injury for COVID-19 and the association between extrapulmonary organ injury and the prognosis of COVID-19 patients. Methods This is a single-center, retrospective, observational study and total 349 confirmed COVID-19 patients admitted to Tongji Hospital from January 25 to February 25, 2020 were enrolled. We collected demographic, clinical, laboratory and treatment data from electronic medical records. Potential risk factors for extrapulmonary organ injury of COVID-19 patients were analyzed by a multivariable binary logistic model, and multivariable COX proportional hazard regression model was used for survival analysis in the patients with extrapulmonary organ injury. Results Average age of the included patients was 61.73±14.64 years. In the final logistic model, variables including aged 60 or older (OR 1.826, 95% CI 1.060-3.142), ARDS (OR 2.748, 95% CI 1.051-7.185), lymphocytes count lower than 1.1 ×109/L (OR 0.478, 95% CI 0.240-0.949), level of IL-6 greater than 7 pg/ml (OR 1.664, 95% CI 1.005-2.751) and D-Dimer greater than 0.5 μg/ml (OR 2.190, 95% CI 1.176-4.084) were significantly associated with the extrapulmonary organ injury. Kaplan-Meier curve and log-rank test showed that the probabilities of survival for patients with extrapulmonary organ injury were significantly lower than those without extrapulmonary organ injury.between Multivariate COX proportional hazards model showed that only myocardial injury (P=0.000, HR: 5.068, 95% CI: 2.728-9.417) and circulatory system injury (P=0.000, HR: 4.076, 95% CI: 2.216-7.498) were the independent factors associated with COVID-19 patients’ poor prognosis. Conclusion Older age, lymphocytopenia, high level of D-Dimer and IL-6 and the severity of lung injury were the high-risk factors of extrapulmonary organ injury in COVID-19 patients. Myocardial and circulatory system injury were the most important risk factors related to poor outcomes of COVID-19 patients. It may help clinicians to identify extrapulmonary organ injury early and provide relevant management strategy.