The COVID-19 pandemic has great consequences on mental health. We aimed to assess medical students’ psychological condition and influencing factors as a baseline evidence for interventions promoting their mental wellbeing. We conducted an online survey from April 8 to April 18, 2020 to examine the mental health of medical students by the nine-item Patient Health Questionnaire, seven-item Generalized Anxiety Disorder Scale, seven-item Insomnia Severity Index, and six-item Kessler psychological distress scale. Factors associated with mental health outcomes were identified by multivariable logistic regression analysis. Five hundred forty-nine students completed the survey; 341 (62.3%), 410 (74.6%), 344 (62.6%), and 379 (69%) reported anxiety, depression, insomnia, and distress, respectively. Female students, living in high COVID-19 prevalence locations, more than 25 days confinement, psychiatric consult history, and being in a preclinical level of studies had higher median scores and severe symptom levels. Multivariable logistic regression showed female gender as a risk factor for severe symptoms of anxiety (odds ratio [OR]: 1.653; 95% CI: 1.020–2.679; P = 0.042), depression (OR: 2.167; 95% CI: 1.435–3.271; P < 0.001), insomnia (OR: 1.830; 95% CI: 1.176–2.847; P = 0.007), and distress (OR: 1.994; 95% CI: 1.338–2.972; P = 0.001); preclinical level of enrollment as a risk factor for depression (OR: 0.679; 95% CI: 0.521–0.885; P = 0.004), insomnia (OR: 0.720; 95% CI: 0.545–0.949; P = 0.02), and distress (OR: 0.650; 95% CI: 0.499–0.847; P = 0.001), whereas living in high COVID-19 prevalence locations was a risk factor for severe anxiety (OR: 1.628; 95% CI: 1.090–2.432; P = 0.017) and depression (OR: 1.438; 95% CI: 1.002–2.097; P = 0.05). Currently, medical students experience high levels of mental health symptoms, especially female students, those at a preclinical level and living in regions with a high prevalence of COVID-19 cases. Screening for mental health issues, psychological support, and long-term follow-up could alleviate the burden and protect future physicians.