The coronavirus disease 2019 (COVID-19) epidemic has brought major challenges to the global health system, and influenza is also a problem that cannot be ignored. We aimed to explore and compare the clinical characteristics of COVID-19 and influenza to deepen the understanding of these two diseases and provide some guidance for clinicians to make differential diagnoses. We searched PubMed, Embase and Web of Science for articles and performed a meta-analysis using Stata 14.0 with a random-effects model. This meta-analysis was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. One hundred articles involving 226,913 COVID-19 patients and 201,617 influenza patients were included, and all the articles included patients with these two diseases as experimental and control groups. Compared to influenza, COVID-19 was more common among men (OR = 1.46, 95% CI: 1.23–1.74) and people with a higher body mass index (MD = 1.43, 95% CI: 1.09–1.77). The proportion of current smokers among COVID-19 patients was lower than that among influenza patients (OR = 0.25, 95% CI: 0.18–0.33). Patients with COVID-19 had longer stays in the hospital (MD = 3.20, 95% CI: 2.58–3.82) and ICU (MD = 3.10, 95% CI: 1.44–4.76), required mechanical ventilation more frequently (OR = 2.30, 95% CI: 1.77–3.00), and had higher mortality (OR = 2.22, 95% CI: 1.93–2.55). We also found significant differences in some blood parameters between the two groups of patients. Upper respiratory symptoms were