Background Severe infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or influenza virus can cause patients to be admitted to intensive care units (ICUs). It is necessary to understand the differences in clinical characteristics and outcomes between these two types of critically ill patients. Methods We searched Embase, PubMed, and Web of Science for articles and performed a meta-analysis using Stata 14.0 with a random-effects model. This paper was written in strict accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Results Thirty-five articles involving 131,692 ICU patients with coronavirus disease 2019 (COVID-19) and 30,286 ICU patients with influenza were included in our meta-analysis. Compared with influenza patients, COVID-19 patients were more likely to be male (odds ratio (OR) = 1.75, 95% CI: 1.54-1.99) and older (standardized mean difference (SMD) = 0.16, 95% CI: 0.03-0.29). In terms of laboratory test results, COVID-19 patients had higher lymphocyte (SMD = 0.38, 95% CI: 0.17-0.59) and platelet counts (SMD = 0.52, 95% CI: 0.29-0.75) but lower creatinine (SMD = −0.29, 95% CI: −0.55-0.03) and procalcitonin levels (SMD = −0.78, 95% CI: −1.11-0.46). Diabetes (SMD = 1.27, 95% CI: 1.08-1.48) and hypertension (SMD = 1.30, 95% CI: 1.05-1.60) were more prevalent in COVID-19 patients, while influenza patients were more likely to have cancer (OR = 0.52, 95% CI: 0.44-0.62), cirrhosis (OR = 0.52, 95% CI: 0.44-0.62), immunodepression (OR = 0.38, 95% CI: 0.25-0.58), and chronic pulmonary diseases (OR = 0.35, 95% CI: 0.24-0.52). We also found that patients with COVID-19 had longer ICU stays (SMD = 0.20, 95% CI: 0.05-0.34), were more likely to develop acute respiratory distress syndrome (OR = 4.90, 95% CI: 2.77-8.64), and had higher mortality (OR = 1.35, 95% CI: 1.17-1.55). Conclusions There are some differences in the basic characteristics, comorbidities, laboratory test results and complications between ICU patients with COVID-19 and ICU patients with influenza. Critically ill patients with COVID-19 often require more medical resources and have worse clinical outcomes. PROSPERO Registration Number: CRD42023452238