Background In December 2019, Coronavirus Disease 2019 (COVID-19) outbreak was reported from Wuhan, China. Information on the clinical progress and prognosis of COVID-19 was not thoroughly described. We described the clinical courses and prognosis in COVID-19 patients. Methods Retrospective case series of COVID-19 patients from Zhongnan Hospital of Wuhan University in Wuhan, and Xi-shui Hospital, Hubei Province, China, up to February 10, 2020. Epidemiological, demographic and clinical data were collected. Clinical progress of survivors and non-survivors were compared. Risk factors for death were analyzed. Results A total of 107 discharged patients with COVID-19 were enrolled. The clinical progression of COVID-19 presented as a tri-phasic pattern. Week 1 after illness onset was characterized by fever, cough, dyspnea, lymphopenia and radiological multilobar pulmonary infiltrates. In severe cases, thrombocytopenia, acute kidney injury, acute myocardial injury or adult respiratory distress syndrome were observed. During week 2, in mild cases, fever, cough and systemic symptoms began to resolve and platelet count rose to normal range, but lymphopenia persisted. In severe cases, leukocytosis, neutrophilia and deteriorating multi-organ dysfunction were dominant. By week 3, mild cases had clinically resolved except for lymphopenia. However, severe cases showed persistent lymphopenia, severe acute respiratory dyspnea syndrome , refractory shock, anuric acute kidney injury, coagulopathy, thrombocytopenia and death. Older age and male sex were independent risk factors for poor outcome of the illness. Conclusions A period of 7–13 days after illness onset is the critical stage in COVID-19 progression. Age and male gender were independent risk factors for death of COVID-19.