Background: The COVID-19 pandemic has profoundly impacted mental health, particularly exacerbating conditions such as depression, anxiety, insomnia, post-traumatic stress disorder (PTSD), and emotional disorders among hospitalized patients. This study examined the prevalence of COVID-19-related mental health issues and risk factors in hospitalized patients affiliated with MNUMS, compared to a control group. Aim: To assess the prevalence of mental health disorders such as depression, anxiety, insomnia, and post-traumatic stress disorder (PTSD), and to identify their associated risk factors. Materials and Methods: The study was conducted at hospitals under MNUMS, including the Mongolian-Japanese Hospital, Central Hospital, and the National Center for Maternal and Child Health. A total of 552 participants (399 case group, 153 control group) who were hospitalized were included. Depression (PHQ-9≥10), anxiety (GAD-7≥10), insomnia (ISI≥15), and PTSD (PCL-5≥33) were assessed using standardized scales. Analysis was performed using chi-square tests and binary logistic regression (crude odds ratio [cOR]/adjusted odds ratio [aOR], 95% confidence interval [CI]), adjusted for group, age, and sex. Results: In the case group, depression (23.1% vs. 13.7%, p=0.015, cOR=1.884 [1.124-3.156]), anxiety (16.8% vs. 11.1%, p=0.096), and any mental disorder (18.0% vs. 13.7%, p=0.225) were higher, while insomnia was lower (19.5% vs. 30.1%, p=0.008). PTSD was low overall (1.8% vs. 0.7%, p=0.333). Risk factors included female sex (p<0.001, cOR=0.362 for depression in males), younger age (p=0.004), unemployment (p=0.017), and prior trauma (p<0.001). COVID-19 symptoms (difficulty breathing) increased the risk of depression (p<0.001, cOR=2.828 [1.708-4.682]). Conclusion Hospitalization for COVID-19 increases the risk of depression and anxiety, modulated by demographic, clinical, and socioeconomic factors. Targeted interventions for vulnerable groups are essential.