Background: The novel 2019 coronavirus (COVID-19) has caused a global pandemic, and often leads to 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 and the association between extrapulmonary organ injury and the prognosis in COVID-19 patients. Methods: We implemented a single-center, retrospective, observational study, in which a total of 349 confirmed COVID-19 patients admitted to Tongji Hospital from January 25, 2020, 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 hazards regression model was used for survival analysis in the patients with extrapulmonary organ injury. Results: The average age of the included patients was 61.73 +/- 14.64 years. In the final logistic model, variables including aged 60 or older [odds ratio (OR) 1.826, 95% confidence interval (CI): 1.060-3.142], acute respiratory distress syndrome (ARDS) (OR 2.748, 95% CI: 1.051-7.185), lymphocytes count lower than 1.1x10(9)/L (OR 0.478, 95% CI: 0.240-0.949), level of interleukin-6 (IL-6) greater than 7 pg/mL (OR 1.664, 95% CI: 1.005-2.751) and D-Dimer greater than 0.5 mu g/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. 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. Conclusions: 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 initiate appropriate treatment.