Background The COVID-19 pandemic is a major health crisis has led to adverse mental health consequences in the general public, medical staff, and individual in self isolation. In order to stop transmission of the virus and save lives, Fangcang shelter hospitals were developed and used for the first time in China. However, there is no research on mental health problems in Fangcang shelter hospitals patients during the COVID-19 outbreak. The aim of this study was to survey the prevalence and major influencing factors of anxiety, depression among the hospitalized Coronavirus Disease 2019 (COVID-19) cases in Fangcang shelter hospital. Methods From February 23rd, 2020, to February 26th, 2020, we obtained the information of demographic data, clinical symptoms, and assessed the mental health status, sleep quality by using an online questionnaire including self-rating anxiety scale (SAS), self-rating depressive scale (SDS) and pittsburgh sleep quality index (PSQI) at Jianghan Fangcang shelter hospital. We assessed the prevalence of anxiety, depression symptoms and poor sleep quality via the scores of SAS, SDS and PSQI. We explored the influencing factors of anxiety and depression in COVID-19 patients using multivariable logistic regression models. Results We collected data from 307 COVID-19 patients in Jianghan Fangcang shelter hospital. The prevalence of anxiety, depression symptoms were 18.6% and 13.4%, respectively. Poor Sleep quality, number of current physical symptoms ≥ 2 were independent risk factors for anxiety symptoms (P < 0.05); female, family member confirmed COVID-19, number of current physical symptoms ≥ 2 were independent risk factors for depression symptoms (P < 0.05). PSQI scores were significant positively associate with SAS scores and SDS scores (P ༜ 0.05). Conclusions Anxiety and depression are common among the COVID-19 patients in Fangcang shelter hospital. Those with more current physical symptoms, poor sleep quality are more likely to have anxiety. Females, those with their family members diagnosed with COVID-19, more current physical symptoms are more vulnerable to depression symptom. Our findings can be used to formulate targeted psychological interventions to reduce adverse psychological impacts in Fangcang shelter hospital during the outbreak of epidemic disease in the future.