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Background The issue of population aging is becoming increasingly significant, accompanied by a rise in the number of elderly individuals experiencing comorbid chronic diseases. This study undertakes a comprehensive synthesis and analysis of evidence regarding the prevalence and influencing factors of chronic disease comorbidities among the elderly, utilizing systematic review and meta-analysis methodologies. Methods This study included cross-sectional research on the prevalence and influencing factors of chronic disease comorbidities in the elderly. A systematic search was conducted across several databases, including PubMed, Web of Science, Embase, Cochrane Library, CNKI, WANFANG, CBM, and VIP, covering the period from the establishment of each database until August 15, 2024. The methodological quality of the included studies was evaluated using the AHRQ tool. A random effects model was employed to calculate the pooled effect size for the prevalence of chronic disease comorbidities among the elderly. To assess potential publication bias, funnel plots and Egger tests were utilized. Subgroup analyses were conducted to investigate significant factors contributing to heterogeneity. Additionally, sensitivity analyses were performed to evaluate the robustness of the meta-analysis results. All statistical tests were executed using Stata 18.0 software. Results This study included a total of 49 medium to high-quality documents, encompassing 729,043 elderly respondents. The findings indicated that the prevalence of chronic disease comorbidities among the elderly was 46.0% (95% CI = 38.0–55.0%, I² = 99.98%, P = 0.000). The summary results of the subgroup analysis are as follows: men (0.41, 95% CI = 0.35–0.47) versus women (0.48, 95% CI = 0.41–0.55); respondents from China (0.40, 95% CI = 0.33–0.47) compared to those from other countries (0.53, 95% CI = 0.44–0.63); surveys conducted before 2020 (0.49, 95% CI = 0.39–0.59) versus those conducted after 2020 (0.39, 95% CI = 0.30–0.49). Furthermore, the identified risk factors influencing the comorbidity of chronic diseases in the elderly include age (≥70 years), gender (female), body mass index (BMI ≥ 28 kg/m²), education level (at least junior high school), marital status (single, widowed, or divorced), and higher income levels. Conclusion Research indicates that approximately half of older adults experience multiple chronic diseases simultaneously. The modifiable risk factors contributing to the development of chronic comorbidities in the elderly primarily include obesity, low educational attainment, poor marital status, and the income level is low. The findings of this study offer significant insights for policymakers aimed at mitigating the burden of chronic disease comorbidities in the elderly and enhancing their quality of life.