Background: Currently, China has an increasingly aging population. However, the prevalence of metabolic syndrome (MetS) in this high-risk population for metabolic diseases remains unknown. To investigate the age and gender specific prevalence and associated factors of MetS in Chinese middle-aged and elderly population, we did the study on it. Methods: Data were retrieved from China Health and Retirement Longitudinal Study (CHARLS) and subjected to descriptive statistics. Further, univariate logistic regression was used to evaluate the relevant factors, and then multivariate logistic regression was selected to construct the final model. Results: In present study, a total of 10,834 participants were included. The overall prevalence of MetS was 32.97% as defined by International Diabetes Federation and 29.75% under National Cholesterol Education Program - The Adult Treatment Panel III criteria. With aging, prevalence of MetS descended in males, while ascended in females. In the >70 years old group, the prevalence of MetS was three times higher in females than that in males (50.43% versus 16.03%). Across all age groups and sexes, the prevalence of MetS in urban areas was significantly higher than in rural areas. In addition, regardless of gender, the prevalence was highest for those living in the north region (28.41% for males & 51.74% for females) and lowest for those living in the southwest region (13.91% for males & 31.58% for females). Finally, two specific correlates, afternoon nap and blood urea nitrogen (BUN), were identified in present study (P < 0.05). Conclusion: The prevalence of MetS varied in different age groups, sexes, living areas and regions and was associated with afternoon nap and BUN.